Some jet2 flights were weather diversions, some were pre ordained to reduce the overcrowding in the terminal because the French Border Force can't process the passports quick enough. The previous Saturday, some folks were taking 4 hours from landing to leaving the baggage hall. One flight diverted as they had nowhere to put any more folks.
Not sure whether it's a personnel issue. I came through Lyon and the passport check took no longer than pre Brexit, excepting the 5 secs to stamp it.