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Code page doesn't support line numbers over 999, numbering "restarts" from 000.

Diff versions in History could show line numbers too.

This doesn't happen with me, it's correctly showing the amount of code lines

Maybe it depends from browser (I use Waterfox Classic).

No problem with Waterfox Classic for me too for JS script.
Just it seems not have line number for UserCSS code.
By example:
Flickr WideScreen - BigONE

Have you a test link?

https://greasyforks.org/en/scripts/407284-imdb-scout-mod/code

Same on Pale Moon too.

I understand the (no)problem now:
The line number work perfectly, but the start of 1000 it's just hidden:
so, you see just "000".
In fact, if you watch better:
".000"
2 Screenshots with your example at line 999/1000:
1 - without CSS tweak: line number truncated.
2 - with a CSS tweak which reveal the whole line number...