No you'll not be in trouble, so don't worry about that.

Here's the news update previously issued by UKBA

Changes to the requirements for biometric residence permits

Here's a key extract:-
If you are from outside the European Economic Area or Switzerland and, while you are in the UK, you are granted permission to stay for more than 6 months on or after 1 December 2012, you must apply for a biometric residence permit (if you have not already done so). If you are affected by the change we will write to you about how to apply for your biometric residence permit.
So you can see you are not affected.
You'll apply for your Biometric Residence Permit when you make application for FLR(M)

Hope this puts your mind at rest