I had a litter of pups vet checked and given the all clear at 7 weeks old but one puppy has just gone for his 2nd vaccination and the vet says one baby tooth,a lower tooth is on the inside of his mouth instead of the outside so when the big teeth come through it will be the same so he needs it removed.My vet never picked up on this and im so angry.Can this be missed at 7 weeks?If this is the case how soon does the tooth need to be removed?

Puppy teeth can be knocked out of alignment,  as well as come through out of place,  so if the first vet didn't notice,  this may e what has happened

Don't panic though,  I have seen this corrected successfully with Ball Therapy and without removing any teeth!

Have a read here
A Removeable Orthodontic Device for Lingually Displaced Canines in young dogs

In addition,  I have seen adult teeth come through either side of the puppy teeth,  so it isn't guaranteed that the new tooth will come through wrongly positioned.

Just remember,  though,  that this would count as a cosmetic procedure for the purposes of showing ;-)