I have no idea on troubleshooting PhantomJS but none of those packages look like they would be responsible for causing your issues (at least not directly).

Also according to the PhantomJS downloads page it is a static built binary that is self-contained so should not depend on any system files (beyond fonts; and except at build time).

Having said that, it does note a dependence on some specific glibc versions - IIRC relatively recently there have been security updates to libc. Considering that it's such a fundamental package to the system having security flaws in that would have wide ranging consequences so downgrading would be a very short term last resort and I wouldn't do it on an internet facing machine...

Have you updated PhantonJS at all? If so perhaps that's your issue? If not, perhaps that's your issue!? Personally the first thing I would do is migrate your server to a v14.x base and update PhantomJS to the latest version. If that doesn't work or you continue to have issues, then I would contact the PhantomJS community to assist troubleshooting. Perhaps there is even a known issue (with a workaround)!? Or perhaps it's just broken on the old version of Debian (TurnKey v13.x is based on Debian Wheezy which is pretty old)?

Personally I wouldn't do what you are suggesting (at least not until you've upgraded to v14.x and updating PhantomJS). Regardless, to explicitly answer your questions; you can install an older version of a package easily with apt, e.g.:

apt-get install <package-name>=<version>

Using dpkg as an example:

apt-get install dpkg=1.16.17

If you want to disable auto security updates. Do that by commenting out (adding a '#' at the start of) the line in /etc/cron.d/cron-apt that looks something like this:

40 14 * * * root test -x /usr/sbin/cron-apt && /usr/sbin/cron-apt

and then restart cron:

service cron restart

I would not recommend holding a version of a package with a security updates available until you fully understand the consequences of leaving the security issues unpatched. I.e. read the DSA (Debian Security Announcement) to get an understanding of what the security risk is, how critical it is, how you may be able to mitigate or workaround it. If you decide you are ok with pinning an insecure version then the currently installed version of a package can be held with apt like this:

apt-mark hold <package-name>

Then to undo:

apt-mark unhold <package-name>

Note, dpkg can do the same thing:

echo "<package-name> hold" | dpkg --set-selections

Undo:

echo "<package-name> install" | dpkg --set-selections