Hard Disk will not boot internally.

I have a Mac mini from 2009 (A1283) that I wanted to upgrade the HDD in. I bought a 1TB Western Digital Black and installed it. When I went to install Mac OS I found that the disk wouldn't show up in Disk Utility. After Trying a few more times I decided to try and use a USB adaptor and format the disk on my iMac, the drive showed up and formatted succesfully. Popped it back into the Mac mini and once again it couldn't see it. I put the drive back into the USB adaptor and connected it to the Mac mini and it was detected with no issue. Installed El Capitan and after updating to the latest version (10.11.6) I put it back into the Mac mini. This time it could see the disk but always fails booting (crossed circle), at some point I decided to try a different disk and used an SSD I had with Yosemite on it. It booted with no issue.

At this point I'm not sure what to do, a fresh HDD that I have since tested with other machines will not work in this Mac mini but an SSD works with not problem.

TLDR: HDD fails to boot with SATA but SSD works fine.