Is it possible that the error is related to something else?

No.

By default, Perl can open 2048 files concurrently. Excluding the 3 standard files (stdin,stdout,stderr) that leaves 2045 for program use:

perl -E"say(),open $fh[$_], '>', qq[file$_] or die $! for 1 .. 1e5"
1
2
3
...
2040
2041
2042
2043
2044
2045
2046
Too many open files at -e line 1.
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Any tips on how to debug this?

You could modify all the open and close lines something like this:

open $fh, .... or die ...;
close $fh;
[download]

To

open $fh, ... and printf( LOG "%s(%u) opening %u\n", __FILE__, __LINE_
+_, fileno( $fh ) ) or die ...;
printf( LOG "%s(%u) closing %u\n", __FILE__, __LINE__, fileno( $fh ) )
+ and close $fh;
[download]

Once the program fails it should be simple to find which opens do not have or are not reaching their associated close statements.