Inclusion is so so important, and I am glad we're way past the days of 'sending the special kids' off somewhere else so that they don't disrupt the 'normal kids'. That attitude makes me sick. BUT forcing a child into a situation they aren't happy with or able to cope with isn't inclusion.
It really depends why he's being 'excluded'. If it's because he's distracting the other children and it's almost as a punishment then no that is not ok. Not at all and I would remove my child from a setting that did that.
If it's because that's how he's happy and calm, because he cannot cope with the larger groups and it's specifically for his benefit then that's fine, better than fine really it's beneficial.
If all that's happening is he needs a movement break - not uncommon at all especially at THREE YEARS OLD - then they just need to let him get up for a minute then gently guide him back. Egg timers work well for this, any visual aid will likely help. So 'Sam, you can stand up and get all of your wiggles out until the egg timer runs out and then it's time to sit down and eat our sandwich please' is better than just ordering him to sit down nicely and expecting him to be capable of doing so. And that's if he has that level of understanding and no learning difficulties, he may well have OP hasn't clarified. Would have worked with DD but she has no learning difficulties and is cognitively very able. He's also at an age where very basic comic strips might help to teach him the social skills, why and how we sit nicely at mealtimes although I would be gobsmacked if it worked well with a child so young. It'll be a work in progress for a long while I expect. Does he have a visual timetable at the setting OP? One of those would probably help as well. So he knows what's coming Now, Then and Later and can mentally prepare for the transition to lunchtime.
As I said my dd (who has an EHCP because of her ASD) eats her lunch separately from the class in reception because she cannot cope with the big group as close quarters or the echoey noisy hall. She and the other little girl with ASD (and an EHCP) eat in a nice middle area with their alternating 1-1s. They then go and join in with the others for outside play. Both me and the other little girls mum are happy with this (we talk!) as are the children. They eat well - essential for their concentration in the afternoon. - , in comfort, not stressed or overloaded. perfectly happy. But they are being well supported and the school is catering to their additional needs by doing this. They are not sending them off somewhere else because they're a pain in the bum (although no doubt they would be if expected to sit at the table in the big hall with the others).
OP feel free to PM if you want a chat. I've not long gone through the EHCP process with mine and I know how hard it is especially when parents of NT children (or worse, early years 'professionals') don't get it!