I have the default mailbox size set to warn users at 6500MB. But users are not being limited. I used the get-Mailbox -Identity to check the size of a user mailbox and here's what I got:
IssueWarningQuota : unlimited
ProhibitSendQuota : unlimited
ProhibitSendReceiveQuota : unlimited
The user does have the storage quota set to "Use mailbox database size"