I think you have drive issues here that need fixing.
First you'll need to create a bootable external drive. I would recommend getting a USB thumb drive and then using Disk Utility delete the current FAT partition on the thumb drive and create a GUID / Mac OS Extended (Journaled) drive. Then using the OS installer (from the App store) install a fresh OS on the thumb drive. The Last thing I would do here is copy over the OS installer to the thumb drive.
OK, now we have what we need to boot up your system and if needed the OS installer to re-install the OS.
But before we move on make sure you have a good backup of anything important! As you may find the disk (either) may need reformatting.
Now using the Option key during the boot up you should gain access to the boot manager service. We want to select the USB thumb drive (it will take a bit of time here so don't panic). Once the system is booted up from the thumb drive locate on it Disk Utility. Run Disk Utility and repair both the permissions (you may need to do a few passes) and then Disk repair on both your HD & SSD.
I would also take the time here to move or delete any junk that you have on your disks. The boot up disk (SSD) should have at least 1/3 of it free space so the OS has enough space to work with. The last thing here on cleaning things up is deleting old cache files, log files and error reports. You'll need a cleaner App to do this effectively. Checkout the App store to find one if you don't already have one.
OK, so far we've fixed the drives, cleaned out the junk. Now we need to address the way the drive works:
SSD's need a means to clean up freed space. Depending on your drive it may have this as part of its firmware or you'll need a program to enable TRIM services.
HD's are different! they need to be defragmented once and a while. Yes I know everyone tells you its not needed, Rubbish you do! Here you'll need a good tool like: Drive Genius. We run it on our systems yearly and it does make a big difference!
I know its a lot here but its all needed - Good luck!