This has been a bug since I believe 1.9, I'm not too sure when it started. But, this bug has essentially broken flying machine transport.

TO RECREATE:
Construct a flying machine. I cannot show any screenshots as this as this damned site won't allow me to upload any images due to a "missing token".

Stand on any non-slime block in the structure. You will find that you'll constantly clip through the block and snap back on top

After some time of traveling, you'll either be launched off of the flying machine because you touch a slime block through another block, or you'll simply clip through and fall.

EXPECTED RESULT:

The flying machine simply carries you without a problem

This also breaks any elevators designs that make use of horizontal flying machines