The jql autocomplete parser has some weird behaviour around reserved characters see JRA-22927. Full-stops are not an uncommon things in version numbers.

Right now if one has versions 4.0, 4.0.1, 4.1 and 4.2. And types 'affectedVersion = 4.0' 4.1 and 4.2 will still be in the list but there will be an ! at the top of the jql parser box.

If you type 'affectedVersion = "4.0' (note the double-quote (") is not yet closed), the autocomplete list will be winnowed down to just 4.0 and 4.0.1 but there will be an ! at the top of the jql parser box.

If you type 'affectedVersion = ""' and then within the "" type 4.0 the list will be winnowed down to 4.0 and 4.0.1 and the jql parser will keep its tick.

I would expect that all three would behave the same way. With perhaps the first 2 keeping the ! as the value is not quoted correctly.