N.B. I have not updated anything in my OP relative to the v2.1 patch. Some things may be addressed or may not be addressed. If anything has changed, please indicate what has changed in a response.

This thread can be considered a repository for bugs with Trine Enhanced Edition. For my part, with the game completed, what follows below is what I've found. Please note that items in parentheses aren't bugs but oversights/problems nonetheless.

Achievement Bug
'Undead Have Rights, Too' can be triggered without meeting the requirements. On Academy Hallways I killed many enemies with both the Thief's bow and the Knight's sword. It would be fair to say that this was the overwhelming majority of the kills, say +80%. The achievement requires a non-Astral Academy level where no enemies are directly killed though, presumably, they can receive weapon damage from the Thief and Knight.

'Summer Dip' is unable to be unlocked with a character that has the Scales of Fish item. It also cannot be unlocked by switching between characters, at least not once the Scales of Fish item is acquired. The Thief has the item and after a minute it still does not unlock. I switch to the Wizard and wait until his breath bar is almost gone, which is more than the 20 seconds required, then I switch to the Knight and did the same before finally switching back to the Thief. At this point I exited the water and attempted the same, but starting with the Wizard (does not have Scales of Fish). Whether or not this can be unlocked before the Scales of Fish item is acquired is something I do not know.

'Summer Dip' update: after sitting underwater with the Thief, the character with the Scales of Fish item, while typing the above paragraph, the achievement unlocked after I jumped out of the water. This was well over the 20 seconds with the game running, viz. not the pause menu.

General Movement and Combat
The Jump key (Spacebar) will occasionally not take the keyboard input. This is not a keyboard issue, is present in Trine 2 as well and seems to be related to tapping or holding the Jump key to determine jump height or distance.

(Though infinitely better than having only three angles with which to shoot the Thief's grappling hook in Trine, Trine Enhanced Edition suffers from the same issue as Trine 2: the Thief can legitimately shoot her bow in 360-degrees, but is remarkably limited to the direction the grappling hook can fire. While not a bug, this is a fair and important criticism given game mechanics.)

(Wizard's levitate ability still moves slowly and does not build up momentum if the player's movement of the mouse is accelerated.)

(Thief is unable to attach a grappling hook to the Wizard's Box or Plank, but can attach it to the triangular Floating Platform. This is awkward in that the Wizard, if now learning how to make items the Thief can use, is unable to utilise that with other abilities and seemingly in favour of the ability to set the Floating Platform on fire with the Thief's fire arrows or the Knight's fire sword attack.)

Knight's Throw replacement, Magnetic Shield, is able to too easily drop items if the player moves the mouse in any way but slowly. This results in a weaker replacement if this functionality is intended, though making the any character but the Thief functionally weaker is a very strange design decision.

'Wonky physics' a la Left 4 Dead and Left 4 Dead 2 can result in regular enough occurrences of enemies and characters moving faster and jumping higher than seemingly intended. This is particularly noticeable on platforms that fall after a character or enemy touches them, seeming to utilise part of the 'ledge grab', which already functions awkwardly, to mess with the physics and result in the aforementioned.

Flame-spewing skeletons can occasionally spew fire through the Knight's shield. Even if the Knight's shield is already up and the Knight is walking toward the skeleton with the shield up and at the correct angle, the fire will occasionally go through it. Fireball traps also function in the same way, most notably when jumping/falling.

Enemies, at least the weak skeletons, are able to kill themselves by striking their heads against any object when jumping, sometimes once and sometimes twice before the death. This follows for stronger enemies and has been observed on the swinging log in Ruins of the Perished.

If enemies are present during a 'gate scene', viz. a quick cutaway to where a gate, bridge or what have you is opening, enemies can still damage the prone character.

The Wizard is occasionally unable to reliably move weighted objects because they are 'too heavy', resulting in very slow swing times and over much too long a time (e.g. Iron Forge). Related to this, 'heavy revolving platforms' (e.g. Iron Forge) move very slowly and over much too long a time when jumped at to push up, however they move normally when walking on them. This seems to indicate a physics problem with generating force.

Crypt of the Damned
'Boss' is able to walk over a wide gap in the ground. This gap is made by getting the last experience bottles in the area and pulling a switch that moves a trap door to the side and enables characters to go back up instead of using the Thief's grappling hook to swing up the way the player came.

'Boss' seems to be able to turn quicker than before and attack a bit faster. Attacks are difficult (bug?) to block unless they are at just the right angle, however ground-pounding attacks seem to have an issue with going through low blocks. It's particularly frustrating that the Thief can jump and shoot downward in mid-air but the Knight cannot do the same.

Forsaken Dungeons
'Boss' is able to be killed with no danger by using the Thief. I will not reproduce the details because it appears to be an exploit.

Throne of the Lost King
Damage radius of spiked balls in 'cog room' extend slightly beyond their visual representation, resulting in characters taking damage without actually coming into contact with the spiked balls. This is shown by the spiked balls continuing on their path at the same velocity and, being changed to something, the change in velocity marked by touching a character would be shown.

Misc.
(Settings->Configure Controls->Wizard no longer shows that the Wizard can spin objects by pressing A or D. No other control setting alludes to this either.)