What @Lorna says is correct, but it’s only supposed to apply to keys with the *xxx* key caps. The screenshot is showing Keyman Developer. Does this issue arise in the apps as well? Which version of Keyman Developer / Keyman are you using?
Perhaps related to this case, but the font size on the “special” keycap is slightly larger than the usual font size in other keycaps, rendering the special letter I put on the “special” keycap get cut-off. I need to make a screenshot for this later.
Is the font size intentionally set bigger in the “special” keys?