That is because after removing the first "slice", slice number 2 becomes number 1 and when you attempt to remove slice 2 it is actually the original slice 3 that is taken out. In other words in terms of original slice numbers you are removing the first 100 odd-numbered slices, 1,3,5,7,.... Also the slice numbers you quote are inconsistent - there are 101 slices in 0 to 100 and 300 to 400 and you would have 201 left in 100 to 300. Also there is no slice 0 in terms of index numbers.
I'll assume you want to remove the first and last 100 leaving the middle 200. Do this:
A(:,:,[1:100,301:400]) = [];
