This can happen if SpamAssasin is not enabled for mailbox/domain/server. So service itself can be running, but it does not remove of flag the spam.
First make sure that SpamAssasin is running:
Open Plesk > Tools & Settings > Services Management
Next check that it is enabled for mailbox:
Subscriptions > example.com > Mail > [email protected] > Switch on spam filtering for this email address
Or globally in Plesk > Tools & Settings > Mail Server settings
Also you can test it by sending a message containing the following string of characters in message body (in upper case and with no spaces or line breaks):
XJSC4JDBQADN1.NSBN3*2IDNENGTUBE-STANDARD-ANTI-UBE-TEST-EMAILC.34X*
Check the /var/log/maillog
for lines like:
Dec 3 20:52:48 pleskserver spamd[1107]: spamd: identified spam (1000.0/7.0) for [email protected]:110 in 6.1 seconds, 3926 bytes.
These lines show that spam was detected.
Reference article.