Probably just a matter of having the right cutters. Sort of like the difference between a wood and metal saw.
This ain't no amateur operation. The project's geological engineers were fully prepared to bore through the types of rocks and sediments found in that area.
Bertha is the biggest, most sophisticated tunnel boring machine on earth. If the operators only needed to change out the cutter heads, this wouldn't have made the news.
Something tells me that we're never going to get a straight answer on what really stopped the operation.