In current Arma 3 with all available DLC including APEX installed I am getting duplicated missions while playing through the campaigns:

This can be seen in the case of Rising Tensions, Damage Control, Bomos and Supply Network in this case.

I completed Bomos the last time that I played, went into the briefing part of Supply Network and quit there. I am not sure whether Bomos or Supply Network was the last mission shown when I returned this time, but I selected the last one and had to repeat Bomos after which I could continue with Supply Network (which is now in progress). I am not sure when the duplicated missions for the Prologue appeared, but I think I might have had to play one of those missions twice, too. It may not happen always, but did for me. I can't remember any crashes when playing Arma 3. Most missions were played shortly before the release of Apex, a couple of the last ones of East Wind afterwards. The game was always updated to the most current default version through Steam.