I don't think this is technically a "bug".
When they changed the cost for a few upgrades to eliminate the more powerful combinations they seem to have allowed for existing upgrade selections to be preserved which means that a percentage of players will have combinations of upgrades which are now "illegal" but which are maintained because they were grandfathered in due to the fact that they were already in place at the time of the change.
Grandfathering these upgrade combinations is the friendliest, and probably easiest, way to address this sort of situation where you are changing the costs involved on upgrades which are already in use. Using this method you just wait for the players will "illegal" combinations to change them voluntarily after which they must adhere to the new cost structure.
The alternate method would be to forcibly purge the upgrade chosen which would require everyone to reselect their choices and would force everyone to immediately adhere to the new cost structure. Depending on how the system is set up they may not be able to single out "illegal" combinations to be purged, meaning that they need to purge everyone's upgrades or it may just be considered difficult to do the purging on the backend or too inconvenient or upsetting for the community.