You have to rebuild them or you could try to fix them with 'control + G'.
To do this, you have to find the brush first. The compiler will say which brushes u need to fix, example:
Entity 0, Brush 268: degenerate plane
Now go the the editor and load your map, to find brush 268:
Go to the Edit tab, and click at 'find entity / brush' now you can put the brush number (268) and the compiler will show where it is.
Then remake the brush, you can also try to 'snap to grid' it using Control + G. You have to do this with every single bad brush.
You have to find & delete all brushes but is it possible to delete all wrong brushes with a programm or automaticly?
I believe the Rogue's Plugins would work, I don't use it myself:
http://homepage.eircom.net/~kdja4/kdja/Plugins.ace
You can install the plugins by just putting it in: MOHAATools\plugins.
Then you can find these unde rthe plugins tab in the editor.
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Bad brushes are mostly caused by: using the 'drag vertices' tool (V) in a wrong way, rotating brushes, and copy/paste (bad) brushes.