This technically isn't what I would call a bug, more of an accidental happening...

Here it is:

When using a custom window with the debug command, ie, /debug @whois - The debug output, as well as any output generated by script that is directed to a window labelled @whois, will appear on the same window.
Call it a bug, call it a feature, or call it plain annoying, do as you please, but I fall into the 'slightly annoyed' category.

Perhaps the /debug command should be given its own windowing subsystem, and that any window opened up by /debug cannot have 'accidental output' generated to it by any script within mIRC.

How could mIRC differ between "accidental" and "intentional" outputs?

Very simple.

Create a specific method of text output for the debug process, so that it can only be output to screens created for the debug process, and that no other text from other events gets output to it.
This could be via a Debug handle for the window.

I guess as an interim solution, we/I should use /debug @Window.debug

Then someone else would complain because they couldn't echo their code to @debug windows for realtime comparisons.

var %dwname = $+(@debug-,$network,.,$cid)
window %dwname
debug -pt %dwname

Well, that is what I use at least, you don't absolutly need the $network in there, just as long as you have $cid (as that is unique) you are good: $+(@debug-,$cid) I just happen to like seeing the network in the window name.

Edit: debug -pt $+(@debug-,$network,.,$cid) is good enough, I actually have it do window -e on mine (for an edit line, because I like it) and well, I have this perform on connect.

Perhaps a switch to override?