Using Monaspace 1.301 fonts on up-to-date Windows 11, in VS Code 1.104.1, with these settings:

{
    "window.zoomLevel": 0,
    "editor.fontSize": 14,
    "editor.fontFamily": "'Monaspace Argon', monospace",
    "editor.fontLigatures": "'calt', 'cv01' 2"
}

the 'S' is not as tall as other capitals, and the '2' is not as tall as other numbers.

Removing the fontLigatures line entirely does not affect either issue.
Both problems do go away if I use window.zoomLevel of at least 2, or if I set editor.fontSize to e.g. 12 (on any zoom level), or if I switch to Neon.