Permission issues running homebrew scripts

So, I keep getting stuff like this when doing updates, installs, and upgrades. Any ideas?

Molly:Downloads Binary$ brew update
/usr/local/Homebrew/Library/Homebrew/cmd/update.sh: line 78: /usr/bin/tr: Permission denied
/usr/local/Homebrew/Library/Homebrew/cmd/update.sh: line 78: /usr/bin/tr: Permission denied
fatal: cannot exec 'gc': Permission denied
Already up-to-date.
Molly:Downloads Binary$

Do you have a multi-user setup? /usr/bin first in your path? An agressive virus scanner/device manager?

Multi-user setup? Not exactly? Just basic only user on a Mac 10.14.6.

AV scanner? Not really. I’m running Trend Micro and Micro Snitch. But, it would have notified me if something was up.

/usr/bin? Nope. I’ve been trying to muck with that. But, the system default PATH is doesn’t have it as the first.
Molly:database Binary$ echo $PATH
/Users/Binary/anaconda3/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/MacGPG2/bin:/opt/X11/bin:/Library/Frameworks/Mono.framework/Versions/Current/Commands:/usr/local/git/bin:/usr/local/opt/openssl/bin:/Library/Frameworks/Python.framework/Versions/3.7/bin:/usr/local/sbin

That’s odd. What does ls -al /usr/bin/tr tell you?

Molly:~ Binary$ ls -al /usr/bin/tr
-rwxr-xr-x 1 root wheel 27744 May 3 21:04 /usr/bin/tr
Molly:~ Binary$ which tr
/usr/bin/tr
Molly:~ Binary$ id
uid=501(Binary) gid=20(staff) groups=20(staff),501(access_bpf),701(com.apple.sharepoint.group.1),12(everyone),61(localaccounts),79(_appserverusr),80(admin),81(_appserveradm),98(_lpadmin),702(com.apple.sharepoint.group.2),33(_appstore),100(_lpoperator),204(_developer),250(_analyticsusers),395(com.apple.access_ftp),398(com.apple.access_screensharing),399(com.apple.access_ssh)

Any ideas? Still getting the same error for various commands that the update.sh homebrew script uses.