1. Japanese subtitles are completely different from what is said in Japanese dub. Subtitles are optimized for readability and use completely different phrasing, or even terms (for example dub says クイーン ("queen"), sub says 女王 ("jo-oh")).
2. Japanese subtitles and English subtitles are also different, because many lines have to be completely rephrased in order to express them in a (very linguistically distant) language.
3. The furigana (pronounciation hints) in these screenshots is not correct. "困った" is "komatta" not "koma ta". "妻は" is "tsuma wa" not "tsuma ha". If only they used ichi.moe's engine... (disclosure: I'm the author of ichi.moe).
Hopefully it can be fixed, since geminates are one of the most difficult features of Japanese pronunciation for native English speakers to master. Erasing it from the orthography intended to aid beginners certainly doesn't help.
My Japanese comprehension is still very minimal, but wouldn't this be pretty normal? It seems common in manga at least to use kanji for semantic meaning and annotate it with furigana for a foreign word or in-universe term.