The whole problem is people use versioning differently including numbers, letters, date, symbol, terms. Some do just by what they think is right and change it as it is appropriate:
"Hardcoded" - 0.0.0.87 > 0.0.0.95 > 0.0.1 > 0.0.13
"A Spell For All" - 14.9.2.1 > 14.9.3 > 14.9.3.1
"S.H.E.L.T.E.R." - 0.09 > 0.10 (by 'Patreon' post)
"Quidget the Wonderwiener" - 0.2.0 > 0.2.4 > 0.2.56
"My Little Angel" - 0.7 > 0.9 > 1.0b > 1.0f
"The Last Sovereign" - 0.44.5 > 0.45.0 > 0.45.1
"Renryuu: Ascension" - 19.08.24 > 19.09.20 (Using the date)
The whole thing is not uniform, people do not file the same way as each other, yes would make it easier but that is how it works.
It is how some people get confused when a Dev changes their filing/versioning system later, like 0.2.50 > 2.5.0 or remakes a game, but keeps the version, so you have 0.5 > 0.6 no progress (removing is not progress) has been made through the change a clean slate, but keeps it version where it is technically true that a remake would be 0.5 > 0.6 many don't do that as it does confuse people but there are some that do it like that.
...Except while the exact positioning of the versions is different from the version format in the case of Hardcoded and A Spell For All, and Renryuu Ascension obviously because it's not actually using a versioning system (just using decimals to separate the date of release in filename and carrying that over, and that gets placed in the version section here on F95), they all use the same basic system I described. Hardcoded and A Spell For All are just more granular in how they've written out their version numbers. My Little Angel is finished, so it's 1.0; "b, "c", "d", "e", and "f" are appended for bugfix releases to the complete edition, using the letter format as a secondary scale subordinate to the primary scale of the version number.
Devs changing filing/versioning systems can cause issue in the moment they change it, yes. Going from 0.09 to 0.10 is not changing versioning systems. Writing their 0.10 as 0.1 is incorrectly writing their version number as if it was an actual decimal.
If a game gets remade in a new system from scratch, that's a major update worth a version integer increase even if no player-facing content was added. If the game was being slowly converted over to another system as development continued in the original, and gets released as that new system once the conversion is finished, though, the dev might not see the work done to finalize the change of system as being a major update. As I already said, with extremely obvious hyperbolic numbers, version numbers aren't about how much player-facing content is in the release.