This is most likely due to the fact that you have OPCache enabled, which is actually no problem.
You will have to clean the OPCache's cache after new code has been submitted, this is because PHP code is cached in the FPM worker and will not refresh until you say it should.
In case of a deployment, you can either use these lines to refresh the FPM worker (to your deploy script):
echo "" | sudo -S service php7.1-fpm reload
In case of WordPress or any other PHP application you can reload through Ploi's UI inside the PHP tab, click "Reload PHP worker" then you're all set!