Yeah this is wild. Not to beat a dead horse, but I've been having the same exact issues. I'm running a 50/50 Steelers TT, and my safeties are gassed after 2-3 plays max, even when playing in coverage (not blitzing). My 92 Captain Eric Berry (SS2) is yellow after *only* the kickoff. My 94 Cover Athletes Polamalu is gassed after 2-3 plays on defense and gets subbed out for literally the ENTIRE GAME. My edge rushers (92 Porter Sr, 94 TJ Watt) are also gassed after 2-3 plays. I mean it's legitimately everybody on my defense aside from maybe Mean Joe Greene and my outside corners for the most part. Also important to note, I don't play Dollar/Dime/etc. I play primarily 3-4, 4-4 and Nickel.
Also, semi-related, but I've been having stamina issues on OFFENSE too. My HB and OL are tired after just a few plays. No, I'm not running hurry up/no huddle either. Not sure how many others are experiencing issues on the offensive side too, but I know there's at least a few that have posted about it on Xwitter.