Part of the skill in dealing with TUPE is knowing when it applies, and the implication of its application.
Often it will be obvious; if you are selling or buying a business, or if you are outsourcing (or in-sourcing) work. However, it is not always clear meaning the rules are breached.
TUPE is very procedural and, provided you comply with the procedures, you shouldn’t go wrong. The focus is consulting with the affected employees and ensuring you do so in the proper way (e.g. by holding a secret election, if necessary).
What often causes issues is where TUPE applies but the other employer refuses to acknowledge its application. This can lead to your employees being left in limbo with no employer, as you say their employment has transferred, but the new employer refuses to take them on.
Our employment solicitors are very experienced in dealing with TUPE, so will be able to assist with your situation/issues.