I noticed this in ropensci/tinkr#99, but subscript text (at least with pandoc markdown) is converted to strikethrough (with two ~) on roundtrip between markdown -> XML -> markdown

commonmark::markdown_commonmark("H~2~O", extensions = TRUE)
#> [1] "H~~2~~O\n"

^{Created on 2023-08-18 with reprex v2.0.2}