How long has this problem been occurring? If it just started recently, it could just be due to a one-off software glitch so if you haven't just restarted your Note 9 in a while try that. If the problem is still happening after a restart at least you know it's a persistent issue and just just a temporary one.
But if it has been a long-standing issue, than while it could be due to saving to your microSD card is the cause of that odd 'stutter' but keep in mind that would be more of matter of using a more dated, slower card. SD cards come in different 'classes' so if you have a generic, bargain-priced card in a slower class that could be the source of your problem. Any brand-name card within current specs will be more than capable of handling the video read/write needs though (more a 'write' issue than a 'read' issue). Here are a couple of references that provide you with more details:
https://www.sdcard.org/developers/overview/speed_class/
https://www.techspot.com/guides/1591-microsd-buying-guide/
So how old is your microSD card and is it a brand name? As long as the card is in a class faster than your 1920 x 1080 needs it shouldn't be a factor. One unfortunate thing to also keep in mind is the counterfeit market of crap cards is a big, big problem too. As far as appearance a 'fake' card may look legitimate (some even using a logo imitating an established brand) but the storage media inside consists of just junk components, so where you bought your card can be a factor too. But a simple test is to just go into the Settings menu of the camera app and set it back to using internal storage, even just temporarily, to see if that alleviates the problem. If so, and you have an older card, it might be time to get a newer, more capable card. Or try setting your resolution down a bit and see if that makes any difference.
If clearing the camera app's cache didn't make any improvement, you might want to take the time to delve into the camera app's Settings menu. The stock Samsung camera app includes a lot of features that correspond with the camera module inside your Note (a software and hardware combination), so there might be some option on image stabilization or HDR that might be tied to that irritating little jump (i.e. with image stabilization enabled the camera app is trying to overcompensate with the existing lighting, which in this particular instance might not be necessary as you're using a tripod).
Just speculating but I'd be leaning more towards some camera app option to disable/enable that's behind that little 'jump'.