even though i found numerous ways to increase reputation beside sidemissions (terminal, auctions, favour exchange, faction accessory) there are some factions that keep standing "betrayed" and wont allow to go past neutral 0/100
is there something im missing like increase a high amount at a time or finishing a harder mission or just conversation options with that faction?

Nope, this appears to be by design. The idea is that if you ever annoy a faction so much that they start thinking about sending people after you, they will remember this forever and therefore never trust you ever again.

In those situations the most you can repair the rep is back to zero - which is still useful, since that's one less company plotting your death.

I'm not entirely sure what the point of no return is in terms of -ve rep values - just that if the rep indicators say you are marked as an "enemy" (extra red text), then you've crossed that point. ;)

Unfortunately (but also realistically), this doesn't seem to work in reverse for the "trusted" green text. After achieving "trusted" with a company, the "trusted" status does actually remain even if your actual trust level dips below that point - though I assume there is another point (possibly 0 rep?) where this would be cancelled out - but it doesn't appear to actually give you any lingering positive trust (i.e. your actual rep is still used for determining thresholds for rewards etc.).