It is vital that beat triggers are accurately placed at the correct metric location. If a detected transient is slightly off the beat, Beat Detective may assign it, as well as other transients in the selection, to the wrong metric location.
For example, if you have a bass track where a note was intended to be a downbeat, but was played too early, Beat Detective may define its location as occurring a little before the downbeat. If you then separate and conform the clip containing this note, it will be moved to the wrong location. Subsequent clips may be moved to the wrong locations as well.
If a beat trigger is not assigned the correct metric location, relocate it using Identify Trigger.