This is normal. Tiled only writes out properties that are set on the object and not those inherited from the tile, to avoid duplicating data, and to allow a distinction between “not set - should inherit” and “set to a value that happens to match the inherited value”.
You can use the “resolve object types and properties” export option to explicitly set inherited values. This is an export option and only affects exported files, and you should not overwrite your working files with these exports.