Repairing (with repair command or r-key) any upgrading building which is damaged results in way too costly repairing at the same repair speed. Tested with Cybran shields, land factories and people claim it happens with mexes too. Tested on public "balancetesting" version just an hour ago. Did not test with ACUs or SCUs
How to reproduce:
Build a structure that can be upgraded.
Damage or reclaim part of it's health.
Start the upgrade for that structure.
With an engineering unit, repair (either with r-key or repair icon) the structure.
Watch your engineering unit drain all your mass.
Screenshot illustrates!