Yes, the problems you describe are likely just due to not using the API correctly.
Facebook Connect is still very new and does suffer from occasional problems, but in general it is pretty stable and is being implemented by many major sites.
This developer post may be relevant to your problem: (From: http://www.facebook.com/developers/message.php)
Please make sure features are loaded before using Facebook Connect JS APIs
Feb 26, 2009 1:35pm
Almost all Facebook Connect's JS APIs
are loaded asynchronously after
calling FB.init(). Because of the
asynchrous nature, the JS APIs are not
necessaryly available immediately
after making these calls. You should
use FB.ensureInit or
FB.Bootstrap.requireFeatures to ensure
the JS APIs are loaded before using
them.
We have a wiki documentation that
describes this in more detail.
However, we just found out that some
Connect apps were calling Connect JS
API such as FB.Connect.* and
FB.Facebook.* immedidately after
calling FB.init. This approach would
cause intermittent failures because
the functions may not be loaded yet.
Pior to last night's push, we fixed a
bug in our FeatureLoader.js.php where
it was always automatically staring
the asynchourous loading of Connect
features. After the bugs is fixed,
code that were calling JS API before
making they are loaded are more likely
to fail. If you noticed that your
Connect apps are getting function not
defined erros for Connect JS
functions, please check your code to
make sure it is waiting for features
to loaded before using them.