I had 21 energy left, and needed 25 experience to obtain rank 1039. I accomplished this with a round of XTS-Refinement, with the result of a full energy bar of 13980. My next action was to use my rank points to buy 6 engineers and 4 tactical officers. Suddenly, my energy bar was at 27/13986. It appears that my 6 energy (from buying engineers) were added to my old energy total (21) instead of to my new energy total.

Has anyone else encountered a problem like this?

To confirm, this is not a browser/refresh issue. Switching to a different computer, I do not have enough energy to complete a round of 'Controlling the Anomaly'.