max_nesting_level has nothing to do with how many functions you call, but how many nested levels of function calls you have. max_nesting_level protects things like:
function a()
{
a();
}
a();
Without Xdebug's max_nesting_level, this will make PHP crash because it runs out of stack space.
The max limit for the setting depends on he operating system, but in general anything over 2500 seems to be too high.
In order to make sure Xdebug's max_nesting_level isn't hit during running of your script, you probably need to change how your code works (ie, don't do nesting or recursive function calls). Because I do no know your code, I of course can't say whether you might just have hit a bug in it.
cheers,
Derick