This is discussed on the FAQ page but probably worth an airing here on prime time. All versions of Yatca up to now only receive updates and replies from users you follow. Replies sent to you by other users are not collected. This is very much by design. The rationale was that receiving replies from strangers (?) would require Yatca to make a second request to the Twitter servers on each polling cycle which would adversely affect your data usage and battery life.
The feature is however increasingly supported by other Twitter clients and it has been heavily requested for Yatca. So it will be included in the next release of Yatca as an optional behaviour that is enabled by default. To be completely accurate, what will actually be added is support for receiving mentions from users you don’t follow. A mention is a recently introduced Twitter concept for a tweet that includes your screen name anywhere within its text (and therefore includes all replies).