I've had this issue in my current game and after much reloading of old saves, I think I have it pinned down.
The issue arises in the first building/unit/repair you choose after completing the repair of a pillaged district (but not building). It occurs twice in the following series of saves (the last two are in a reply), affecting my city of Rouen.
On each occasion when you go to choose something new to produce after the district repair is complete, the number of hammers required for each option looks normal, but the turns to complete are inflated, as if there were actually more hammers required. When the project is selected, it shows as 0/XXX where XXX is the normal required hammers, but again with the inflated turns. But after ending the turn, it comes back with one less turn to complete (as would be expected) but with progress now negative. i.e. the build is starting from a negative number of hammers.
The following saves use the CQUI mod, with the relevant version also attached. I realize that the devs may not want to look at modded games but it is a UI mod only (not sure it even affects saves?) and the sequence of saves captures this issue perfectly.
Turn 255: I am at war with Philip. In the city of Rouen, I was building a university (yes, in the middle of a war). My aqueduct, campus and library have been pillaged. On the production queue, the university (in production) shows as 162/337, the campus as 45/235 (I thought pillage was supposed to do less damage than that), the aqueduct as 37/277 and the library as 60/120. All times to repair are consistent with those numbers and my production.
Turn 260: The war has ended. I stopped production of the university and am repairing the campus (up to 60/235 - 12 turns remaining @ 15.1ppt). The pillaged library and partially complete university do not show in the production window, but the tooltip on the site acknowledges the pillaged library.
Turn 270: No major developments. Campus repair now at 209/235, two turns remaining.
Turn 272: The first hiccup. The campus repair is complete and I have chosen to repair the library. It shows as 60/120… but with 17 turns to complete… enough turns for 245 production. Turns to complete for all other buildings and the later-era units are also inflated, as if they require about 180 more production than they should do.
Turn 273: After ending turn 272 it came back with the library requiring 16 turns (down by one as expected) but with progress -101/120. But the production times for everything else were back to normal. So (prior to the save) I switched to completing the university instead (now requiring only 9 turns, rather than the 22 it said on the turn 272 save).
Turn 283: The university has been completed and I’ve gone back to repairing the library, now -81/120 and requiring 13 turns at my slightly increased production rate.
Turn 290: Library repair continues, now 28/120 and requiring 6 turns.
Turn 300: The ridiculous library repair is now complete and I have started repairing the aqueduct, which is at 117/277, consistent with me having worked on it for four turns from its Turn 255 pillaged state. i.e. the repair hasn’t gotten any longer despite being chosen after the library repair (hence the conclusion that it only occurs after district repairs, see below).
Turn 308: I didn’t initially save at this point, but I stepped through again from turn 300 to replicate what happened after completing the aqueduct repair. At this point, there is one more turn required to complete the aqueduct repair. Going into the city screen, all the production times for potential prjects look fine, except for some short build times for older units, which I’ve seen raised as a query elsewhere.
Turn 309. The aqueduct repair is complete… and we’re back to the same situation as Turn 272. All the production times are inflated. I’ve chosen an industrial district and it shows as 0/495, but with a production time that will produce 728 hammers.
Turn 310. As Yogi Berra would say, it’s déjà vu all over again. 30 turns remaining for my industrial district with progress of -208/495. But if I want to switch to something different, production times are back to normal.
So the two affected “builds” were the library repair (chosen after repairing the campus) and the industrial district (chosen after repairing the aqueduct). But it didn’t matter what I chose – all builds showed inflated build times immediately after those district repairs were completed. Also once those builds were chosen and end-turn processed, the negative starting point for that project was locked in – I could switch to something else (like I did to complete the university) and it would go normally – but when I came back to the affected project, it picked up again from where I left it, i.e. with negative progress.
I’m not sure whether it’s possible that this is related to the fact that the district pillaging itself did more damage than I thought it was supposed to – unless they are supposed to be different to the 25% of initial production required to repair pillaged buildings?