"Stuttering" after refuelling.

When refuelling 1996 3ltr. diesel SC van, I've experienced brief episodes of the engine stuttering/bunnyhopping after driving some 15-20 km. On several occasions, a puff of black smoke has been visible prior to this happening. Could there be deposits of something being disturbed in fuel tank on refuelling which then are being drawn in to fuel inlet line? This doesn't happen every time we refuel, but it's becoming more frequent. Fuel filter is not yet due for replacement, but feel this would be first in line for remedial attention. Any suggestions?

Yes fuel filter might be good to replace, although it may not resolve the issue.
But if you drained the tank significantly one time, it could be deep enough to suck in the residue.

Please check, or have a mechanic check, if there is anything wrong with the ventilation of the tank.
Are you using the official fuel cap or have you been using a different one recently?
Or you could pullover when it starts to do the stuttering and loosen the fuel cap a bit to make sure air can get by.

There is an output in the filler, and there should be some air hoses too I think, but I'm not sure how or where these actually run.

Another thought is the fuel return line, but that will probably not lead to this issue.