Hi, Sorry about that. I am using the SFC3 Upgrade Mod 3.2 (outdated I know) and looks like I have patch v534 unofficial.
The issue was that too many ships were destroyed even though some had survived (starbase + planet + fleet) so I was in command of around 10 ships.
The solution was to force most of them to stay back and use one or 2 for a distraction while I handle everything pretty much by myself.
Off topic: Came across an interesting topic here in regards to empire tiles colors, so I did a little modding and came up with a better color scheme (for my color blindness). I've been disassembling Birth of the Federation for years alongside other code analysts in the AFC community as well, I have a feeling a LOT can be done with this game, with the right knowledge.