GTK is unable to produce output at non-integer scales. Given the dependence of GNOME on GTK, a technique called oversampling is used, both in X (via xrandr, Ubuntu implemented a GUI for this) and in Wayland. This first commands the underlying toolkit to render at an integer scale (typically 2x) and then samples the output in order to scale it down to the target fractional scale. This technique degrades font quality to some extent but, most importantly, is severely demanding on hardware. Suppose you have a UHD screen, this is 3840 pixels width, if you wanted a scale of 125% you would need to produce 3840 x 2 / 1.25 = 6144 pixels instead. Considering both dimensions you are increasing the load (2 / 1.25)^2 = 2.56 times. As you can see, this will be worse the closer your target scale is to 100%. Of course, at exactly 100% you just stop rendering everything twice as large, so it's cheaper, but to get 101% (not that anyone would do that) you have to increase the load by a factor of almost 4. Now imagine having two or three screens doing this at the same time.
Some toolkits as Qt are able to directly produce output at a fractional scale, which is not only much more efficient but also renders crisper fonts.
I can't tell if what you experience is related to the kind of overhead I just described, but stuttering and reduced FPS are typical symptoms. Also reduced battery life and an overall less "smooth" system. This is worse using fractional scaling in X than it is in Wayland, but the problem exists in both cases.
