Bare version numbers are glob. If that was in Cargo.toml you were not doing what you thought you were doing.
Presumably OP's workspace contain multiple binary crates, between which dependencies aren't currently unified. The binaries may however access the same file/database/shared state. If the dependencies are not kept in lockstep, this can result in communication errors: semver guarantees are generally reliable for the direct callers of an API, but I/O behavior tend to change on minor/patch updates all the time.