Anything that stops the cylinder firing properly will cause a little splash back ,
And if you are using single filters its more noticeable because it has very little distance to travel to wet the filter
Same thing was happening to my yzf 750 and it was a bloked idle circuit,
The fuel wasn't getting through on one cylinder just splashing back.
The other three were carrying it hence the bad running and every so often it would catch and backfire .
As I said there is many reasons for a cylinder to missfire this is just the cheapest,
Plugs, leads, coils, all should be tested before expecting the timing ,values etc.
I have written this with my phone so sorry if its bad grammar.Chris