We have two Neos. Both have had or have your problem.
The first one for the first few weeks had what felt like a rumbling, bumping at low wattages (like 50-90 watts). It was most pronounced at about 60 watts with a slow cadence. It came at other wattages as well. It was BEFORE we did the firmware update to get road feel. After we did the firmware update for road feel it remained a problem anyway. It felt (after we got road feel update) a bit like a very mild version of cobbles - kind of a mild bumping rumbling through the pedals. We did not do anything to fix it, and it gradually went away so that now it is essentially never there at all. That Neo is now totally smooth and silky at all wattages we do (never over 1000 watts for us).
The Neo was so good compared to the old Bushido we got a second so we both have one.
The second Neo had the same problem, but it was quite a bit worse. If we did moderate wattages (say 250-350) up a steep hill (100% slope turned on, 78 kg rider) in a low gear it was VERY strong rumbling/vibration through the pedals. This was a newer unit which shipped with the road feel firmware update already on it. It also had the same mild vibration in the pedals at lower wattages as the first Neo. We have now had this second one for a month or two and the problem has much reduced on its own. However, on some rides it seems more pronounced than on other rides.
Also, on the second Neo the power reported to Zwift fluctuates more than on the first Neo. During a workout in ERG mode we can see the power trail is quite bumpy on the second Neo, while on the first it is very smooth. On the first (now smooth without the vibration) in Erg power is maybe +/- 4 watts at 150 watt ERG. On the 2nd same workout at 150 watts it fluctuates more like +/- 8 watts. I don’t know if this is related.
We have not taken off the wheel (a special tool is required), but from Shane MIller’s video it seems that perhaps just loosening the bolts and then tightening them up again might perhaps help. Maybe a thing to try on our second one…