SymptomsParallels Panel uses MailEnable Standard 1.986 as a mail server component.
How the issue looks? For example, a mailbox quota set to 25600Kb (Parallels Panel, Domains, some domain, Mail accounts, some mailbox, Mailbox, the "Mailbox quota" field with limited size by the "Enter size" value). But the mailbox usage, which is shown in the Resource usage page (Parallels Panel, Domains, some domain, Resource usage) may be much more than 25600 Kb. Also, in the MailEnable Administrator snap-in (named MailEnable.msc and located in the MailEnable installation folder, the Bin subfolder - for Panel shipped version it should be the %plesk_dir%\Mail Servers\Mail Enable\Bin path) the mailbox quota is set properly and even mailbox over usage is detected. However mail messages may be sent to the mailbox and not rejected.