Funes Mori made a very bright start to his career at Goodison Park, but his performances have dipped in quality since.
The Argentine has struggled since being given regular action after Phil Jagielka picked up an injury, and Thompson believes that the centre-back could have become over-confident.
“I think Funes Mori has started to get found out,” Thompson said.
“Once you start playing more games in the team, you start feeling more confident and taking more chances. You don’t cover as much.”
Everton went unbeaten in the first 13 matches that Funes Mori played for them, but since that record has been broken his performances have been below par.
The Toffees have leaked goals this season, and Funes Mori’s partnership with John Stones has not looked particularly solid.
It is likely that the former River Plate man will now drop out of the team in the near future, with Jagielka nearing a return.
The England international has missed over a month’s worth of action with injury, but he could make his comeback in Everton’s FA Cup match against Dagenham and Redbridge on Saturday.