I ran into the same issue back in October last year, you can read about my findings and replies after here: V1.38 Bug reporting - #411 by DevilinPixy. This issue does not only affect portals, but anything that uses the same mechanic (charge/repair). This includes Hydrophonic Trays, Crashed Freighter Containers, Autonomous Mining Units, Atmospheric Harvesters and alike.
At the time I was not the only one who ran into this issue, there had been multiple reports. The issue has never been fixed. After some extensive research I had done, I concluded it to be caused by an issue with the save system. I could only fix it by rolling back about 50 hours of game play, which I never did. @zsigmond back then, gave me some hope of this possibly getting fixed by itself. Rolling back is still no guarantee either, as the issue may introduce itself again at some point. Starting fresh is another option, but similarly no guarantee.
For me it ruined the fun back then, and in all honesty, I never continued to play as much anymore. I have yet to go to a next Galaxy, which may fix it, but is quite a choice to make. It would make sense to possibly get fixed that way, as it allows for your save to be cleaned up quite a bit.
A true game breaker in my opinion. Never got a reply after sending in several reports of my findings. This honestly needs to be fixed and I truly hope it will be with the next update. It will likely not fix my current save, but I am willing to start fresh again, being assured to not run into this again.