I had this problem, but solved it by referencing the instance's copy of phpunit, so instead of running phpunit, run:
vendor/phpunit/phpunit/phpunit
...so I have an alias for that purpose (my personal shortcut is pu):
# in ~/.bash_profile
alias pu='vendor/phpunit/phpunit/phpunit'
...and make sure to run it from the project root. I'm unsure why I had to do this or even where I found that solution, but like I said, that made it work for me.