Input filters (#tags @usernames)

The Twitter input filters for #tags and @usernames work globally for the entire site.
This could be by design, because this is the way the filters work.

Anyway: If you enable the filters twitter URLs are generated for all @usernames even if they are used in comments or where ever. Hashtags are relatively save because they are not used so ofter in other context than Twitter. The @username syntax is used often in comments though.

Is there a way to prevent that?