One possibility is if you left a previous game before it had finished, and had damaged some bases there, then while you were playing your next game those bases might have got destroyed by someone else still in that game.
If it was this, it should show up in the after battle reports (from the Messages tab in hangar) if you look at the previous games results (i.e. having destroyed more bases then you remembered when you left)
It might have to do with if you damaged the base but did not destroy it and then someone else did the last damage and destroyed it perhaps. Or if you’re using napalm it might be the initial impact damage and time based fire damage are counted differently somehow counting it as two different basses by accident?
Either way it sounds like a bug that might need to be reported, not sure though. You can bug report it here (just search a bit first so that you don’t report something that is already reported and known about): (Gaijin.net // Issues)