Imagine a sequence in the DNA like this: TAAAAAAAAAAAACAAAAAAAAAAG. The way sequencing worked is the DNA is split into small parts and then they are aligned back together. But if we split the sequence above we might get these pieces: AAAAAA AAAAAA AAACAA AAAAAG TAAAAA. You know the first and last letter of each piece overlaps, but due to the high repetition count of A there is no way to figure out what the proper order is.

With new techniques you generate much longer pieces, so there is much less confusion.