I found a fun bug with the Antiproton Bose Einstein Condensate and Positron Bose Einstein Condensate containers that I don't think I've seen mentioned here.
Build a ship with two or more antiproton or two or more positron containers (any combination of size, so long as they're the same particle type).
While in the VAB, set the amount of one of the containers to any value; set the amount of the other containers to zero.
Launch the vessel
Open the fuel transfer windows for the tanks, and click "Out" on the tank that has antimatter in it.
Watch the amount in the full tank fall, and the amount in the empty tanks rise (as expected).
As soon as the transfer is complete... notice that the tank that was emptying during the transfer is now full again with the original amount, and the other tanks now contain the combined amount that was in the original full tank.
Recover the vessel, which now has twice the amount of antimatter as when it was launched.
PROFIT!
This only happens after the vessel is newly launched for the first transfer between multiple antimatter tanks. Subsequent transfers between tanks after the first transfer doesn't further change the total amount of antimatter contained in the tanks. If you launch the vessel (but don't fly it off the launch pad), switch to another active vessel, then switch back to the vessel on the launch pad, the antimatter doubling bug still occurs for the first fuel transfer; if you launch the vessel, complete one transfer, then switch to another active vessel and back, then the bug doesn't reoccur. If you launch the ship off the pad and do the first transfer in flight, the bug doesn't occur.
This is using KSPIE 1.29.2 on KSP 1.12.2. Not sure if this has already been fixed for later versions of KSPIE.