Congrats! Lax auditors or not, a 99 is a score you should be proud of.
Root cause investigations are always somewhat difficult with auditors. Some will claim you haven't gone far enough despite pages of documentation, others will literally accept a two sentence statement as sufficient. Unfortunately, there is quite a bit of leeway and interpretations there. Though for such a finding, it seems like the auditor just needed to "find something" since it doesn't look good on them to write 100's very often.
Specifically to your example of the weeds growing, sure the root cause can be laid at your landscaper's feet. But it would also occur to me that there was some type of check that should've been performed by QA to make sure the landscaper is completing the tasks required, which is where internal audit programs can be developed to catch the issues before your auditor does.