When a font is set for the "default" face in the init.el file.
For example, like this:

(set-face-attribute 'default nil
   :font "Fira Code"
   :weight 'regular
   :height 170)

This messes up the font selection for various latin and all ipa characters.
Despite the configured font supporting the characters which are typed,
Emacs selects a different font for them, this results in visually jarring
text or sometimes failed composition.

For example see in 1.png
All of the letters except ṇ (#x1E47) are in Fira Code while it is in Latin
Modern Mono despite Fira Code supporting it.
Below it t̪ (t + #x32A) is not composed properly because while 't' is in
FiraCode #x32A is in Step Regular.

Note: This does not happen with emacs -Q

Thanks