I had it happen to me once with HP.
I equipped armour plating, then after a couple of games I took it off as it was too easy - also a couple of opponents quit at the first turn, so I figured less but HP full resist looked a bit less scary and was about as powerful
Back to the point; after removing the armour plates I had too many HP - not the whole amount, and putting back the plates gave me the correct calculation again.
Dunno if that helps track down the bug, the one mentioned in the OP could be a similar thing after removing energy modules?