The indents.scm file is missing a rule for anonymous functions, which is causing incorrect auto-indentation when writing callbacks inside functions.
Example Gif:

Example:
lines[i] = lines:gsub(pattern, function(m)
if true then
return m
end
end) -- <-- This `end)` call will get indented like so inline with
-- the if statements `end` when inserting a new line above it
Fix:
Add (function_definition "end" @end) @indent to indents.scm
I having issues getting it the extensions to load into Zed on windows... but I did manually change the current indents.scm file from the current extension version downloaded able from Zed and it works as expected. When I get to load as a Dev Extension to confirm it works still, I will create a PR with the change.
Edit: Attached is a gif of the behavior as well