There's absolutely no reason to believe that foreach has anything to do with this. I suspect the last $abifiles doesn't contains what you think it does. Perhaps there's trailing white space or a newline. Temporarily add the following inside the loop:

use Data::Dumper;
local $Data::Dumper::Useqq = 1;
local $Data::Dumper::Terse = 1;
local $Data::Dumper::Indent = 0;
print("$abifiles = ", Dumper($abifiles), "\n");
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You should also change:

$abif->open_abif($abifiles);
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to

$abif->open_abif($abifiles)
  or die("Can't open or read file \"$abifiles\". "
        ." Possible error: $!\n");
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From looking at the source, $! is accurate if no other error messages is displayed. (It can even be accurate if another error message is displayed.)