If you set the speed multiplier to something crazy high, like 100, then when your science packs run out you still get 100 seconds of research progress even if you only had enough for 5 seconds. Don't set the speed too high if this bothers you. Might fix later.
Also, the packs might get drained very slightly different from what they should due to rounding errors. For example, you can end up with a red pack with 0.001% durability after crafting 10 red packs and researching automation. This doesn't really affect anything.
Crafting "Technological Progress!" in assemblers is possible. I'll try to disable it later. But they just disappear when you pick them up so it doesn't affect anything.
Edited this post to remove some fixed bugs