Issues with side missions in open world areas

TLDR: I complete side missions on Acts 2 and 3 but they don’t register as “complete”, being stuck in parts of the game, or having to skip them all together (PC Steam version)

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Hello. I am having an issue with the PC/Steam version of the game where side missions are functionally complete (such as with Jack’s upgrades) but they don’t actually “register” as complete. Reloading the previous checkpoint does not work.

I ran into this issue once the first time through (around November) but after reloading the last checkpoint, it worked.

But now playing on experienced it happened twice already, One of them in act 2, when trying to get one of the upgrades, and the game does not let ypu advance if you don’t pick up the upgrade, had to reload previous checkpoint and skip this one after many tries (same one I had an issue with the first time, but this time it didn’t work).

Second time just happened, on act 3, when going into the pump station, and the engineer from the first returns at the end and gives you the upgrade for Jack with the surge protector for the cloaking device. I pick it up, or order Jack to pick it up, and nothing happens, the objective is never completed so I also had to skip it after trying many times. Curiously, I recently had similar issues with Gears of War 3 replaying that on 360, many bugged checkpoints, maybe we should have proper saves and the ability to see a list of all the game’s checkpoints and access them whenever we want?

All other instances of this happening I see on the internet, are from around September-October 2019 when the game came out, one would assume that after many updates and a full blown story dlc, these issues would be resolved but apparently not.

Anything I can do about this?