There may be multiple issues rather than a single one, and they may be caused by object properties rather than by path-finding algorithms, but from the player's point of view it looks like poor AI movement on piers of all kinds, so I will summarize my observations in this single report.

Pier (Metal). Units will only move along the “lanes”, never crossing the metal bordering lines, — even if adjacent objects overlap considerably, — unless some other walkable object is placed above that lines. However, they will happily jump in the water across that metal lines, whenever such opportunity arises. First I thought it (and other issues described below) may only apply to the user-placed objects that are not part of original island, but then noticed that the same things happen on native props as well, such as the docks near Altis International Airport:

The attached screenshot depicts the L-part of the larger pier (that one with a high military cargo post) with some additional objects. Thin colored lines represent unit movement without those user-added objects: as can be seen, AI units will only walk along their initial lanes and may occasionally jump in the water (not just fall accidentally, but jump willingly). When another Pier (Metal) is placed across the lanes slightly above the surface, they will use it to cross the metal lines; the same holds true for Pier (Concrete). However, AI completely disregards Pier Box (that high concrete column): they do not consider it a walkable surface, unless they already happen to be placed on it, or that box slightly protrudes above another object they consider appropriate; however, they will attempt to move away from that object as soon as possible, preferring to jump into water over staying on that prop.

Pier (Concrete). Most favorable by AI, although still not without troubles: sometimes, if a unit is standing on such a block that is totally above dry land, it will refuse to move to another block that is partially above the water, — although it may sometimes help to repeat the order, it usually requires to move the unit to another position before he finally agrees to step on the partially submerged block; once on the submerged block, however, unit have no fear on further movements, but may exhibit “teleportive” behavior, instantly warping between predefined “Position #n” locations when moving across adjacent blocks. The most serious issue is that units standing on the ground outside of such blocks may be reluctant of stepping on the pier at all, even if there is no other way to reach their target, — they do not even consider swimming, but only run in circles around that pier entrance (which smoothly transitions into the ground). Also worth to note is that, since that object has limited height, there is usually water underneath it, and any unit already in the water, when given the order to occupy a predefined position on the block surface, will swim underneath it, — also demonstrating an infinite amount of breath without any air supply.

Pier Box. As already said, AI does not treat this object as walkable; if already placed on such object, units will walk away from it in any direction they seem fit — even not preferring other types of objects nearby, happily jumping into the water. As with other types of pier objects, it is quite surprising how AI not only hesitates to keep away from water, avoiding use of ladders and boarding platforms to get back to a firm surface, and even more so, how AI prefers swimming over walking or running. Nevertheless, more specific to Pier Box objects may be the fact that it, unlike other pier objects, does not have predefined positions for AI to move in, — perhaps those objects may just miss some configuration.

To illustrate the above issues, I have made a small scenario with all three types of pier objects. As Pier (Concrete) is the most AI-friendly, it is used as the on-land entry block in all cases (however in vain), but no more than that: each pier has its primary blocks both on land and in the water. At the end of each pier there is a team leader, while his subordinates are placed in increasing distances from him and should naturally begin to gather around their leader once the simulation starts.

Pier Box (left):

1. Human-controlled leader has no trouble walking anywhere on the pier.
2. The nearest unit that is placed on the block above the water will immediately jump into water and swim towards his leader.
3. The unit that is on the partially submerged block will walk back to the entrance made of Pier (Concrete), jump on the ground and start running in circles around the pier entrance.
4. The unit that is on the pier entrance consisting of Pier (Concrete) will move as closely as possible to his nearest Pier Box, but will not move any further.
5. The unit on the ground will not step on the pier at all, just running in circles around the entrance.

Pier (Concrete) (center):

1. Human-controlled leader has no trouble walking anywhere on the pier.
2. The nearest unit that is placed on the block above the water will move as expected, although teleporting at times and may occasionally jump in the water.
3. The unit that is on the partially submerged block will act similarly to the previous one.
4. The unit that is on the block above the dry land may not want to move at all, depending on his position. However, once in “good” position after additional “Move To” orders, he will behave no different to previous units.
5. The unit on the ground will not step on the pier at all, just running in circles around the entrance.

Pier (Metal) (center):

1. Human-controlled leader has no trouble walking anywhere on the pier.
2. The nearest unit that is placed on the block above the water will move along his lane only, but may want to jump in the water.
3. The unit that is on the partially submerged Pier (Concrete) (not clearly visible on the picture, but he is definitely not on the Pier (Metal) yet) will act like the previous one — after stepping on Pier (Metal), he will move along his lane only; however, as none of them wants to cross the metal lines, he will not be able to move up to the edge and jump in the water (except on pier end, of course).
4. The unit that is on the block above the dry land, will jump to the ground and start running in circles around the pier entrance consisting of Pier (Concrete).
5. The unit on the ground will not step on the pier at all, just running in circles around the entrance.

Back to the L-shaped pier that is part of the island, there are also noticeable glitches with AI units walking through cargo boxes (those without doors) and sand barriers.

As can be seen by having the units to move towards military cargo post, AI will systematically move through metal containers and sometimes finish in the sand boxes. I am aware that it was a known issue in the past, but as far as I understand it should have been fixed since that, and I actually do not see such behavior on land — with the very same containers and sand barriers that are also placed in the mainland part of the docks just near the very same pier.