First I don’t use cloning software any more! Haven’t used it in over 12 years now. What worked back then is just not needed today and it often makes things worse!
But to get to your problem, your system offers a SATA III (6.0 Gb/s) SATA port. When you bought your system it likely had a SATA II (3.0 Gb/s) HDD and the HD SATA cable was only rated for SATA II back then. At the very end of the series Apple did upgrade the drive to a SATA III version and put in a better cable. In any case these old HDD’s never really pushed the SATA I/O channel. Todays SATA III HDD drives with caches (SSHD’s) and SSD’s can push the data flows to the limits of SATA I/O channel.
So like most things the connection between the two devices needs to be able to support the movement they can produce this is where your problem is as the HD SATA cable is not able to do this either because its the older SATA II version or is worn or damaged.
First you’ll need to get a new cable MacBook Pro 13" Unibody (Mid 2012) Hard Drive Cable and here’s the guide you’ll need to follow MacBook Pro 13" Unibody Mid 2012 Hard Drive Cable Replacement.
But even that is not quite enough! You need to place a strip of electricians tape on the uppercase to help protect it from the rough aluminum surface and you need to use care in handling the cable as it’s easy to damaged. Here the thin foil wires within the ribbon can be damaged when folding it. A hard crease will damage it! I use a BIC pen Ink straw to help me form a nice smooth arc where I need to bend the cable.
Your Hard Drive Cable Is A Ticking Time Bomb
So after replacing the cable we still need to undo the poor structure of the data on the drive. Make a backup using TimeMachine. Then setup a OS installer following this How to create a bootable macOS Sierra installer drive I do recommend sticking with Sierra as its file system is still HFS+ If you upgrade to High Sierra or Mojave you’ll end up upgrading it to APFS while I do like the new file system, the older SATA based systems don’t handle it well. Which is why I would stick with Sierra. If you are keen on going higher go directly to Mojave but be careful!
Reformat your drive and then restore your user accounts, apps & data as needed using Migration Assistant.
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