5 years into franchise mode, at times I do see poor clock management by the CPU in 2 minute situations.
I believe the reason for this is likely tied into the way the 2-minute playcalling situation is handled. I notice this because I call plays according to my gameplan. Quite frequently, once I hit the 2-minute mark, I am left with only 1 play to call. That play is the one play I could not delete from my custom playbook. That play is also tied into "safe" or "4-minute offense". Sometimes, if I call a timeout, the 2 minute situational playcalls appear and sometimes.....they don't.
If the same situational playcalling mechanic holds true for the CPU, that certainly could partially explain why we see the 2 minute offense by the CPU handled poorly at times.