This is all because of the inzone instances like Mosg2 said. Depending on what quest you are on you'll see different areas of the zone. You have to "warp" into these areas - it will break follow since you're warping. It's new to WOTLK. Ice and Storm both have a bunch of these areas. Also Dragonblight has a couple - notably one at the gate area where you get the undercity quest. It's really annoying, but it looks like something we have to get used to.