Yes. One in particular was the use of numbers that looked essentially the same. The Babylonians conquered this problem by making sure the character spacing was different for these numbers. This ended the confusion, but only as long as the scribes writing the characters bothered to leave the spaces.

Another problem with the early Babylonian numbering system was not having a number to represent zero. The concept of zero in a numbering system did not exist at that time. And with their sophistication, it is strange that the early Babylonians never invented a symbol like zero to put into the empty positions in their numbering system. The lack of this important placeholder no doubt hampered early Babylonian astronomers and mathematicians from working out certain calculations.