I do not quite understand the question. Versions belong to projects, so when you are working in a project, you only get offered versions that belong to that project.
In other words, if you create or edit an issue (which is always in a project), the affects-version, fix-version and custom-version fields will only offer you the versions that are in that project.
By "while fill the fix version field", do you mean that when you are doing something global, it offers you all versions? For example, if you are searching for issues, they could be in any project, so it's offering you all the versions you might want to search for?
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