Attached are three screenshots taken in 1.11.2, 1.12.2 and 21w05b (first two are modded, but textures are unaffected - if unmodded screenshots are somehow absolutely neccessary let me know) with a comparison of light blue stained glass to light blue wool. Note how in the 1.11 screenshot the glass much more closely matches the wool, but was not changed in 1.12 unlike the wool resulting in this inconsistent coloration.
While light blue is the most obvious example, I'd recommend redoing all 16 colors to get rid of more subtle inconsistencies that exist for other colors.
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Can confirm in 21w06a.
Can confirm in 21w07a.
Can confirm in 21w08b.
Can confirm in 21w11a. Relates to MC-214643.
Can confirm in 21w13a.
Can confirm in 21w16a.
Can confirm in 1.17.
Can confirm in 1.17.1.

Can confirm in 21w39a.
Can confirm this in both 1.17.1 and 21w44a. Here's a side-by-side comparison of the stained glass color scheme before and after the texture update.
[media]Can confirm for 1.18pre-6
Can confirm in 1.18.
Can confirm in 1.18.1
Can confirm in 1.18.2.
Can confirm in 1.19 and 22w24a.
Can confirm in 1.19.2.

In 1.20 Pre-Release 1.
Can confirm for 1.20.1
Also, change the title to include "Stained Glass Pane", I was searching for this issue using the terms "Stained Glass Pane", but couldn't find it.
Following the same palette and consistency of how the textures are made, this would be a possible fix:
[media][media]
In game:
[media]

Can confirm in 24w13a.
Can confirm