Hey there! :)
I would like to ask a quick question about Unity and Blender programs. The animation imports wrong somehow and I cannot figure it out why is that. Any help would be greatly appreciated! Have a nice day!

what exactly is wrong with the animation? Does it fail to import altogether? Does it import animations that are completely wrong or are they mostly correct and just have a few things that are off?  Are you importing the .blend file or exporting and importing some other format?

The file (FBX) imports just fine, but the animations are off. - the idle animation has the feet sliding across the ground and the run animation makes the legs flop around (seemingly as if unity tries to snap the foot to the forward axis)..! 

The rig has been set up as humanoid in unity and is all green. 

Without seeing the animations I wouldn't be able to say for sure by my gut feel is that there are problems with interpolation between keyframes and the representation of rotation between the two platforms. If blender, for example was specifying rotation using euler angles in any order other than x y z for the angles and unity simply converted same orientations at the keyframes to use the order x y z the interpolation would come out differently. When you select the misbehaving bones in blender what do you get in the drop down in the rotation properties? (seen as XYZ Euler in this image)

You can then check the animation curves in unity and see what values it uses to represent the rotation

If unity is using rotatoin.x, rotation.y, and rotation.z and blender is using something different then your rotation interpolation would be weird

This is not a Game Design question. Moving to a more appropriate forum.

Hey @HappyCoder, thank you so much for your help and your detailed answer, I really appreciate it! Have a nice day! 

Although I love the fact that blender is free, I find that it dosent play well with other 3rd party software. When Exporting and Importing I encounter lots of bugs.  Have you though of using Maya LT, its only $35 a month.

Blender will integrate seemlessly with Unity. There's no need for export/import since the .blend format is directly supported. You don't even have to apply your modifiers, so your models remain in an editable state. Just save and go back to Unity. This workflow has saved me hundreds of hours already.