Oh, I know tons such issues:
- improper use of checkpoints
- auto-healing after seeking cover (yes, Halo shield)
- recharge points where you need to run to, to recover health & ammo & other expendable items
- enemies that can cause diseases which you can't heal yourself but need to run ALL the way back to a town or a healer to cure
- cheating AI
- team mates that get in your way and that require too much baby sitting
etc.
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