Polite/technical way to say "user ineptitude"?

Whether this is a good fit for you will depend on the types of ineptitude, but one way of phrasing it which is respectful and which points to the solution as well as describing the problem is:

user training issue

Assuming that you're reporting to management, this gives them a steer towards avoiding these by providing CPD - software or general IT literacy training, perhaps.

It's also easier for the user to agree with if their opinion is consulted. It's more palatable to admit that you "need further training" than to agree that you're "inept" or that you "make regular basic mistakes".

Perhaps this isn't strictly polite but I wanted to include it nonetheless: PEBCAK (Problem Exists Between Chair And Keyboard) or words to that effect

(humorous) Problem Exists Between Chair And Keyboard. Used by technical support helpdesk staff to indicate that the problem with a user’s computer or experience is due to user error.

ID-10T error - an idiot error.
This is perhaps even ruder, bordering on derogatory, nonetheless it is used and it is funny.

Reference

In a polite situation, I would go for a input error/problem/issue.

This would connote an issue with what had been typed in or done by the user without specifically blaming it on them.

I have seen user error used frequently, but that does seem like it could be blaming it on the user, something you might not want to do if they see your report.

A user error is an error made by the human user of a complex system, usually a computer system, in interacting with it.

You may call them inexperienced users to be politically correct; so, you can substitute the reason of user ineptitude with inexperienced user or user inexperience.

ODO:

inexperienced ADJECTIVE

Having little knowledge or experience of a particular thing.

‘an inexperienced driver’

inexperience NOUN

[mass noun] Lack of experience.

‘the accident was due to the inexperience of the driver’