Im not 100% sure what you mean, post a pic or your save file (or setup the cloud saves and tell me the username) and I can look into it.
Account made, JyveAFK.
I spent a run maxing my Void Power Generation capacity to buy some upgrades, but instead of just getting another one extra rank, if you hit max on.. Boost Synth Speed, it goes to 105 instead of 8 like it should have. All the 'max' values didn't just add a single level, but far more than expected for trying to buy one more level.