Yes, it is well-known limitation of the Query,Enrichment, DImension change, etc workflow activities. The wizard code generates this syntax:
instead of: IN ('v1','v2','v3')
given the variable value is: v1,v2,v3
There is no problem with the wizard if the values are typed, only when using variables.
So the only workaround is to replace the Query activity (or Enrichment etc) by a Query def; for instance in a webApp, the webApp var containing a list with values separated by commas, is put in the queryDef where clause as is: