Internal Error: Too many pairs created..?

I have been working on a map filled with a reasonable amount of assets.
Now after a certain while this error popped up, and slowed everything drasticly down.
Launching Unity, debugging the scene, moving/rotating objects,..
This error pops up randomly and freezes my unity for several minutes.
I have been going through several steps trying to debug this error to no avail.
It isn't caused by a certain area in the map, enabling and disabling parts showed me that.(which goes very slow as well.) The error pops up after a certain amount of map parts are enabled.
Now my map is build out of sections properly split in the hierarchy : https://imageshack.com/i/f0AWCfXCj
And the assets are all build out of basic unity colliders.
For more complex assets I made compound colliders existing of multiple objects with box colliders. I tried to be spare with the amount but still keep some realism in the collision areas .
Why I used compound colliders? Cause unity mesh colliders have been nothing but nightmares, and we are dealing with a multiplayer game, where boxes are more easily dealt with than mesh colliders. Example : https://imageshack.com/i/hlcHBaRbj

The game purpose is to have a lot of assets in the scene and be able to interact with those. The amount of assets isn't near a properly filled scene yet... This error had been causing a lot of wasted time and makes working in unity very tedious. In advance, I checked Unity forums before creating this thread and no useful answer/solution has been posted concerning this subject.

I would be really greatful for anyone being able to give me a solution for this. Thanks :)