I just replaced the stock 5400 RPM drive in my i5 mini with a 256GB Crucial M4 and got the issue myself. Fan running full blast (~5500 RPM) constantly. I then tried putting the original HDD back in and still got the same afterward, so not sure if a sensor got knocked loose or what.
I decided to put the M4 back in and let it run that way until I have time to take it to the geniuses, and now the fan isn't maxed out but also iStat pro shows the fan speed at 0 RPM. Not sure if the fan connector got knocked loose or what. Will have to take it back apart to check the connector.
I have ran the Apple diagnostic test on the machine and got this error code:
4SNS/1/C0000008:TMOP
Which supports the theory that a temp sensor isn't working properly.
Anyway, this is all just to say that I have had issues with swapping out the HDD as well.