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Here's how to reproduce it. First an example of how POY correctly detects a faulty command when the faulty commandname does not end with '()', then an example of a Fatal Errot when that same commandname ends with '()'.

$ poy
Information : Welcome to POY 5.1.1 (5.1.1)
Compiled on Mon Nov 17 18:47:49 CET 2014 with parallel off, interface
readline, likelihood off, and concorde off.
Copyright (C) 2011, 2012, 2013, 2014 Andres Varon, Nicholas Lucaroni, Lin
Hong, Ward Wheeler, and the American Museum of Natural History.
POY 5.1.1 comes with ABSOLUTELY NO WARRANTY; This is free software, and you
are welcome to redistribute it under the GNU General Public License Version
2, June 1991.

Information : Setting random seed value to -720489789
Information :
Information :
Information :
Information : For help, type help().

          Enjoy!

Information :
Trees:
Storing 0 trees
Cost Mode: Normal Direct Optimization
poy> thisisnotacomand
Error : Command error between characters 0 and 16:
[left_parenthesis] expected after LIDENT _ (in [plugin])

poy> thisisnotacommand()
Error : There is no command thisisnotacommand
Fatal error: exception Failure("Illegal command thisisnotacommand")

Posted on Google Groups POY4 mailing list, June 18th 2015 :

Good morning everyone
I am running timed search on my desktop using different gap/ts/tv values and for the first two parameters (111, 121) it runs fine but the I get this error at the moment of fusing
Status : Tree Fusing : 4 of 36 --
Assertion failed: (eap1->code == eap2->code), function sankoff_median, file sankoff.c, line 1434.
[0]0:Return code = 0, signaled with Abort trap: 6
[0]1:Return code = 0, signaled with Quit: 3
[0]2:Return code = 0, signaled with Quit: 3
[0]3:Return code = 0, signaled with Quit: 3
[0]4:Return code = 0, signaled with Quit: 3
[0]5:Return code = 0, signaled with Quit: 3
[0]6:Return code = 0, signaled with Quit: 3

I am attaching the .out file

this is the script I am running, which I have use before without any issue:

read ("/Users/lsilva1/desktop/poymol/mim12.fas", "/Users/lsilva1/desktop/poymol/mim16.fas", "/Users/lsilva1/desktop/poymol/mim18.fas", "/Users/lsilva1/desktop/poymol/mim28.fas")
read (prealigned:("/Users/lsilva1/desktop/poymol/mimcoi.fas", tcm: ("221")))
read (prealigned:("/Users/lsilva1/desktop/poymol/mimh3.fas", tcm: ("221")))
transform (tcm:("/users/lsilva1/desktop/poymol/221"))
set (root:"Uroctea_durandi1")
report (data, cross_references, treestats)
search (max_time:00:04:00, min_time:00:00:10, hits:20, memory:gb:8)
select (unique)
report ("Run_221a.tre",trees)
search (max_time:00:04:00, min_time:00:00:10, hits:10, memory:gb:8)
select (unique)
report ("Run_221b.tre",trees)
fuse(iterations:250)
select()
swap(trees:100)
select()
report ("Diagnosis.221.1.txt", diagnosis)
report ("Trees.221.1.tre", trees:(total))
report ("Consensus.221.1.txt", consensus)
report ("Trees.221.1.ps", graphtrees)
report ("Data.221.1.txt", data)
wipe ()

Any help will be highly appreciatted
Thanks and have a great day,
Ligia