There may be core dump in /var/run/.

It has been seen that a file such as php-fpm.core with a large size of 3.3MB is seen.

SSH into the box and remove the core.

Run the following to determine any large files to remove.

du -hd1 /var/run/

Usage of var/run should drop back down to 4%.

It could be that you pushing all the squid cache to RAM for faster processing. Not necessarily a good thing. Frequently-used files will be cached in RAM anyway.