So the glitch is easily caused when using a boat (any variation of boat class) and going up or down a water ramp (more so down [see attachments]). What happens from what I understand is my setup and the boat physics cause a delay on the very edge of the last block of each layer causing the chance to create a stuck instance and then sinking below the block beneath the water level. It doesn't happen as often when going up but is still a possibility too.This did not happen in 1.10 release

My known causes:
►Boat must go slow up or down to cause the issue
►Boat must contain an entity to trigger this effect (in most test runs)

My know preventions:
►Boat must go as fast as possible to prevent such cases (however this doesn't always work)
►Piston speed should be slowed (or increased) to prevent glitch & breaking

1.13 EDIT:
(1) and (2) below refer to each boat glitch here exclusively, not inclusively. Video files will be labeled as such as well with a descriptive video title.

Notice: The bug acts differently in 1.13. (1) It now acts in reverse of the original post; also, as testing this glitch I found another anomaly when boats flow downstream. (2) They now 'jump' as they transition to the lower elevation - this was not noticeable to me in previous versions. I will upload media files to show the glitches that occur now for 1.13 and boats with pistons.

Summary: (1) The glitch like behavior of glitching into blocks now occurs only when going upstream at a slow pace rather than the other way around - a piston system must be present like in the original setup or other variations. (2) A new noticeable bug about boats and elevation change is that boats now randomly jump when going slow downstream and crossing over a gap such as in the original setup. The behavior happens as it begins to hover over the gap and does not seem to correlate to speed as it happens at any speed.

New known causes & anomalies:

►(1) Boats must go slow upstream to phase into blocks
►(2) Boats jump regardless of speed going downstream while changing elevation gaps

New Known preventions:

►(1) Boats must go fast/not stall to prevent glitching into blocks when going upstream.
►(2) No none preventions for this behavior.