The limitation you are encountering with SAM's File Count Monitor is imposed by Microsoft and WMI. Any query that takes longer than "X", or consumes more than "Y" amount of memory will result in timeouts or hard errors. In this case it looks to be a timeout that is causing the number of WMI connections to exceed the quota limit for the server. Increasing the quota would do nothing unfortunately because the violation of memory or time would still occur. In this case the problems appear similar, but are in fact have different causes.
Without proper error handling it's difficult to say for sure what the exact issue the script is having. It may however be resolved by executing the script locally on the host you are trying to monitor using WinRM. Remote execution is far less efficient and can pose other problems.