This might happen when the rewrite rules are flushed. The function insert_with_markers() is using fopen(), but not flock(), so when two pieces of code are calling flush_rewrite_rules() almost at the same time, the second process can write to that file before the first one has closed it.
Check your plugins and your theme for flush_rewrite_rules(), especially those registering custom post types or taxonomies. Some poorly written plugins are calling this on every page load. Disable that plugin.