It has been repeated several times so I can attest that 5Thanos brings bug to 4Thor blue power. Any time Thoress fires her blue, and 5*Thanos is active, she stuns an enemy (as is expected) then stuns one random ally (not expected) and this can be herself.
I have confirmed that whenever Thanos is stunned or downed Thoress’ blue works as expected. So the problem must be with Thanos.
Were you also facing 5* Black Widow at the time? That sounds like her passive. I used 4* Thor against Thanos in Crash of the Mad Titan, and stunned him with no issue.