Just to start off and explain things, I've been having this problem whenever I try and create a fluid domain so I created the simplest example possible. The bounding box seen is not the domain but an exact copy to show the boundaries. I used to have great fluid simulations, now this happens and for some reason any objects set to obstacle are ignored by the fluid, any help would be appreciated Also, if you're having trouble seeing the problem, download the blend file and if it's not my computer causing it locally, you should see that the fluid doesn't collide with the domain properly, there's gaps between all the sides.
Increase the resolution to reduce the gap.
The "glitch" you are experiencing is indeed an artifact of the low-resolution simulation.
The fluid simulation is computed on a grid of N × N × N small cubes, N being your "Final" resolution setting. Every detail of the 3D world, like the boundary location or an obstacle, that is smaller than the diameter of these cubes may be ignored by the simulation. Therefore, you should always expect gaps that are as large as one N-th of the edge of the simulation box.
In your example, you are simulating at N = 65 and visualizing the "Preview" mode at N = 45. Since your gap is around 1/45-th of the box size, it shouldn't be considered a glitch.
Increase your "Final" simulation resolution to ~150 and switch the "Viewport display" to "Final" to see the difference it makes.
Your file simualted at Final = 300 and Viewport display = Final
I, like you, also remember perfect domain to simulation walls parity, but I think I just never noticed the small gap before.
I checked Blender 2.78, 2.79, 2.8, and 2.5, all exhibit the same behaviour.
So I'd say this is as it has always been.