I'm actually surprised that they sent it home without a discussion with you, especially if they had concerns. I've never completed the check without a sit down explanation with a parent even if the child was working at a higher level. That's terrible practice and I'm sorry they worried you.
In my experience a lot of children speak less at nursery than they do at home. It's noisy, they get nervous around lots of others at once, they are busy etc. I also often say I haven't seen a child do something and Mum or Dad will say "oh he does a lot of that at home" it's not unusual and it's a big reason why we work in partnership with parents.
When I do the two year old check I tell parents to remember that we mark conservatively. If a child isn't doing everything in a certain age range then the range above doesn't get highlighted even though he might be doing one of the things in there. I personally like to see a child do something several times before I tick it off (its not really a box ticking exercise but for want of a better phrase). I always think, they can fluke catching a ball once but several catches and they've got it. If they haven't seen it, they haven't seen it but the check is just a snap shot of where he is now, he might do lots of stuff next week or next month.
Not all nurseries are so harsh but we were actively encouraged to mark them down, remember that they have to show value added and he is only very little, he has until the end of his reception year to complete the EYFS.
As he is only two they should be focusing on the Prime Areas, so Personal, Social and Emotional development, Communication and Language and Physical development. Anything recorded in the other areas is a bonus at this stage. Remember that things like not being toilet trained can appear on the check as a dip but that when he gets it he will take a jump up on his next assessment. (Just an example).
But all of this should have been run through with you. It's possible they don't observe very well or that his key worker doesn't have the close relationship that is necessary to hear lots of language. Or that he just gets engrossed in the duplo and doesn't say much. It all takes time, longer than parents think and he really is at the very beginning of his journey. Give the nursery a copy of the assessment he had done and a report of your own so it goes on his records. Don't be worried they are surprised, they probably aren't going to admit they got it wrong.