The Magpies have leaked goals throughout the campaign so far, and they have the worst defensive record of any side in England's top-flight.
Thompson believes part of the problem lies down the right-hand side of the pitch, where Janmaat's attacking intent is leaving Sissoko exposed.
"Janmaat spends half the time attacking," he said. "He's very good at it, but that leaves them open at the back. Sissoko's spotting it and he's thinking 'do I have to go back?' It's leaving massive gaps. There's problems there, between him and Janmaat."
Janmaat has arguably been Newcastle's best performer over the early part of the campaign, but Steve McClaren may have to make sure he doesn't show such a willingness to get forward.
The Magpies cannot continue to concede goals at their current rate if they are to get out of trouble, and it may be that a more secure approach will help them to break out of their slump.
Newcastle have won just once in their first 10 Premier League matches, and they currently sit in 19th place in the Premier League table.
After a derby defeat to Sunderland the pressure is on McClaren to turn things around quickly, with the Magpies' next match coming against Stoke City.