Having burned the midnight oil with a friend trying to find the issues in this simply put awesome mod over the last 2 days all our waking hours this is what ive found so far (apologies if it has been mentioned before or is allready known)
Research:
-Cannot research "Wormhole Navigation" and "Long Distance Jumps" as Empire (the icons are there bud overlapped by existing other research. They can be clicked but no research comes of them thus making multiple star games impossible as youre land locked.
- The research of "phase jump disruption" and "Interstellar networks" seems redundant since you can build those structures off the bat?
Structures:
- Repair Platforms dont seem to actually repair. Theyre also missing the auto-cast icon for repair ie you cant use them manually neither.
- Novalith can be built but not fired.
Ships:
- Antimatter Regen. Edit nm I found out how this works its fine 
- Abilities/Autocast we agree seems to be some but not exclusive to the minidump issues. There is also a lot of ships which becomes bugged/or is bugged for ship abilities and purchases when levelling. Where points cant be spent ect. Especially with Alliance Capitals.
Bugs/Minidump maybes:
- Pirates set as inactive greatly reduces minidumps.
- Minidumps is near impossible to pin-point for us non-programmers as we had a million of them last night and they were utterly random. We even saved the game every 3 mins manually to try and get "as close to a minidump" as we could get but each and every time it would let us game a little longer without exception. We had easily over 100 minidumps during testing over last few days and not once could we replicate it to a fact.
We are confident to say that we agree with you EvilleJedi that it seems to often be involved with abilities and may very well have links to the debris. But we simply dont know. We do not have programming aptitude so its difficult for us to link the events with the "aha!" moment.
So far all testing has been with Alliance and Empire in various forms.
One last wish.
Is there any way the function shield transfer from TEC could be included in some shape or form could be a lot less powerful for all i care or maybe a repair platform that does shields restore or some such? Reason I ask is we found that our flagships massive shields would slowly get eroded by the game by sheer attrition and due to its size would never recharge in any meaningful way even out of combat and as a result we could just watch our ships get eaten down to the bones through the game with no way of doing anything about it 
Hope this helps.
Awesome mod, awesome job. Hope we get rid of the worst mini dumping´.
Going to edit this post with anything I find as summary