Dedupe will not cause this behavior with quotas. Quotas check how much logical data is being stored, and not how much physical space the data is taking.
To see what is going on from the NetApp perspective, you can use the ‘df –s’ command. Output will show used (the amount of physical space used to store the data in the deduped volume), and saved (the amount of space that has been freed as a results of using deduplication). To get the total logical data that is being storage in the deduped volume, you add values of used + saved.