Very true - and it's amplified by inconsistency allowing problems to spread further before being noticed. At work I deal with a lot of Bag-It archives where we have a text manifest of checksums accompanying files on disk and this reliably bites users of tools when something (archive or network transfer tool, Git or SVN, transition to/from a Mac with HFS+, etc.) causes the encoding in the manifest not to match the local filesystem, and the confusion is amplified because some tools will handle normalization differences so the bug report is “why does tool A say this file is missing when Explorer/Finder and tool B say it's fine?”
Canonically equivalent Unicode sequences look the same to machines.
The latter is a much more significant problem, because it can wreak havoc with interoperability.