(1) They mechanically fail to find the clue
Solved by auto-successes on all investigation skills in which your character is a professional.
(2) They don't look for the clue
(3) They don't look for the clue in the right place
(4) They don't look for the clue in the right way
(5) They ignore the clue
(6) They misinterpret the clue
(7) They can't solve the clue
These are all player skill issues.
You seem to think that automatic success at the investigation is the goal of the Gumshoe system.
It. Is. Not.
Gumshoe is all about moving the skill test from the characters onto the players. It's about testing player skill, not character skills through rolls.
If the Keeper says "As you enter the room, you see a desk with papers scattered all over it," and the players immediately go "There's nothing here, I leave." Then they were the cause of 3,4,5 occurring, not the system.
When you misinterpret the clue, you're still going to look for leads for more information. Even if you are totally wrong, you're going to be going somewhere and doing something that will give you more information. Having a lead not pan out because you made a mistake is very, very informative to any investigator. Not to mention the possibility of getting other information while crossing a bad interpretation off the list.
GUMSHOE and its designers claim, repeatedly, to solve the entire "cannot solve clue" problem by fixing #1.
Not at all. They claim that you'll never have the problem of not getting the information you need
because of a die roll. They specifically call out the meat of the game as being deciding what to do with the information you do get.
In short, it's a focus on player skill.
Which just renders the entire "auto-find clue" mechanic into redundant complexity.
The goal isn't to make 2-7 automatically go away and thus make dealing with 1 to be redundant. In fact, the goal is
to focus on them. The players need to decide where to look, how to look, who to talk to, how to approach them, what the clues mean and where they should go for more information.
I think the issues you have with the system are the direct result of expecting it to do the exact opposite of what it does and from misinterpreting what you've heard about the system to arrive at your false expectations.