Can you provide the exact text of the commands you are running? In the description above it’s a little hard to tell what’s going on; I think you use “>” as the last character of your prompt, but I’m not sure.
This seems to be working OK for me:
bash-4.3$ diff <(ls -l) <(ls -al)
1c1,3
< total 304
---
> total 336
> drwxr-xr-x 2 TSJLC PDUSER 8192 Oct 19 09:59 .
> drwxr-xr-x 5 TSJLC PDUSER 8192 Oct 18 17:17 ..
bash-4.3$
However, I may be using a slightly different version of bash:
bash-4.3$ bash --version
GNU bash, version 4.3.48(2)-release (i370-ibm-openedition)
Copyright (C) 2013 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software; you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
bash-4.3$