I just experienced this issue right now (or perhaps, more accurately, just noticed it) for the first time. I’m at Stage 4, Part 6 and have been for about 5 days. Usually I have one of my Sims start a Workshop shift before I go to bed so that it’s complete by the time I wake up. About 15 minutes ago, I started the shift and exited the game. I then reopened the game 10 minutes after that and my day changed in-game. After claiming my rewards, I went back to my Sim in the Workshop shift and noticed that the time left in his shift had increased from ~5 hours and 45 minutes to ~7 hours and 45 minutes. I was very confused and frustrated. I spent real life money on packs to upgrade the shop and if all my Eco shifts have been taking longer than they should, that’s extremely unfair. I was wondering why it seemed like my Sims were taking too long to do Workshop shifts and now I see the reason why.
On the rare occasion that I stay playing the game continuously while a Workshop shift is in progress, and use energy refills and cupcakes to decrease the time, I do not believe the shift time increases. It is only upon exiting the game (i.e.: when I start a shift before going to sleep, exit the game, and come back in the morning) that the shift time increases, as others have mentioned here.