Encountered: Trying to upgrade my diner two diner sized for final upgrade which costs 1125caps. I have exactly 1225 but when I confirm the upgrade it responds with "You do not have enough caps".

Yup. Just rush a room with very low incident chance, or level a dweller up. Not sure why it bugs out on this but seen this one before. Pretty harmless, just a bit annoying.

Had a look at the code today, and it appears that it's because of a rouding issue. Caps are registered with 2 decimals after the comma (or dot, if in US).