What might be the reason for licence compliance violation?
One possible cause might be that someone created a sample database using db2sampl. The sample database contains both of these artefacts:

]$ db2 -x "select tabschema, tabname, type, clustered 
           from syscat.tables 
           where type = 'S' or clustered = 'Y'"

DB2INST1    ADEFUSR    S    -        
DB2INST1    EMPMDC     T    Y


It appears as if something in the instance is flipped during create of sample database, dropping the sample database does not help, the violation persists.

As @Chris Aldrich points out in the comment, db2licm -x does a reset of the license report:

DB2 Workgroup Server Edition   In compliance


Out of curiosity I created 1 MQT to see if the violation re-appears. So far it has not. It's now more than 12 hours since I created the MQT and I'm still in compliance. 

I'm still puzzled by how the licence compliance mechanism works, but I'll add another question about that.