E.B.
Is it possible they are flea bites?
Where are the marks on him?
Flea bites can appear anywhere on the body....but tend to show up on trunk and belly around waist line...and then on legs.
It is a shot in the dark....that is my grand guess without seeing them though.
They tend to be flat or slightly raise....my kids dont itch with them and they normally disappear within 12 to 24 hours.
I say though ALWAYS air on the side of caution. If you think it could be a reaction to the shots maybe he should go get checked out....always better to be safe rather then sorry when it is something worse.