I find it remarkable how poor Belichick's record is against teams coached by his former assistants.
I think that is actually quite understandable. They know how he thinks. They know what he prioritizes. They know what adjustments he makes. They know his strengths and weaknesses. They know the underlying logic he has that makes him predictable to his inner circle even if the rest of the world can't figure out the patterns.
The reverse is not necessarily true. BB might have picked up some of Flores thinking process while Flores was his assistant, but being Flores wasn't making the decisions there was less BB could learn about Flores than Flores could learn about BB.
Also players. The day the Dolphins hired Flores the Dolphins scouting knowledge of the Patriots players probably quintupled. Flores knew more about the strengths and weaknesses of Tom Brady than the Dolphins entire scouting and coaching department. BB did not learn a single new thing about the Dolphin's roster on that day.
But the Dolphins learned what the Patriot's scouting reports said about them. And if the Patriots scouting report says "player X has this tell." Then the Dolphins can exploit that by specifically designing a play where the Dolphins player does the tell and does something different.
And to a limited extent it may be because they treat the game different. For Flores week 2 and 17 were probably the two most important games of the season. The two games he thought about more than any others during the off-season and pre-season. For BB they were just two games on this schedule.
The poor record he has is 14-14 when facing former assistants/players. Which is below his norm but really isn't actually poor, it is average.