I got a problem white the cusom fields option
i have 12 main and 2888 sub categories in total and when i tray to setup cusutom field it only saves the first 10-12 categories depending on the order of the categories
 
is ther a field in php wher i can setup field limit?
or is a bug in my end

Anything above 500 categories at all is too much.
Try to increase php max inputs i.e to 15k

so this is php memory  problem not php limitation in some file ?
im on vps

Anything above 500 categories at all is too much.
Try to increase php max inputs i.e to 15k

End users will not experience issue with many categories, until you show them all somewhere
Problem is usually in backoffice.
Anyway you looks to be far bellow your limits...

Issue is in max inputs those can be part of one form. In your case 1 category = 1 input, so at least 5k should be good.