Max Greatest Annoyances #5: it is possible to save a patch using one of the ‘reserved’ names
If you save your patch using the name of one of the existing Max objects, this object can not be instantiated anymore. For example, if you save your patch as message.maxpat, you will lose messages functionality in all of your patches. I fully understand why this happens, but this happens again and again (ask the support guys!), because it is impossible to memorise all of the Max object names.
I think user-friendly environment should give user a warning in case if he is trying to save the patch using one of the reserved names.

Max Greatest Annoyances #1: messages are not finalised by pressing Enter
Max Greatest Annoyances #2: Max tabbed window grows in size every time you open/close the sidebar
Max Greatest Annoyances #3: new objects are created right on top of the others
Max Greatest Annoyances #4: newly created attrui objects size is too small
Max Greatest Annoyances #6: difficult to transform (change, re-instantiate) graphical Max objects
Max Greatest Annoyances #7: the documentation is fragmented, full of typos and somewhat outdated
Max Greatest Annoyances #8: outdated JavaScript version used in js and jsui objects
a warning (or a more explanatory error message, at the least) would be good and/or more newb friendly, indeed ! I see how putting a warning at time of save would be extremely difficult.
I think this can just be chalked up to good house-keeping with files.
Just like it's good housekeeping to not use spaces in file names so that they can be called elsewhere, it's good house-keeping to have a specific file name format. I always put the current date at the beginning of my patches for example, or my initials as a "library name" in the beginning of my abstractions.
Mr. Grossman has some good advice there, I think.
A related annoyance is when C74 starts using a user's abstraction names without warning, something I grumbled about here: https://cycling74.com/forums/%22palblocks-mxo%22-mysterioiusly-appearing-instead-of-abstraction