Blocked heater matrix

Good Afternoon all,
Hoping to get some advice from you gents....

or ladies (phew, close one.)

Vehicle Info.
2015 1.6 VW Golf S Bluemotion diesel
Mileage 4 months ago: 40,000.
Current mileage: 43,500

Ok, here goes,
About 4 months ago I had the water pump and timing belt changed at my local VW dealership, then approx. 1 month ago I noticed that my heaters weren't working (I know I should have taken action sooner, but the truth is at this time of year it wasn't causing an inconvenience and you know how it goes, always something more important to do instead.)
So, about a week ago I happen to mention my no heater situation to an ex-mechanic friend of mine, he opened the bonnet and immediately noticed the fluid in my cooler bottle had gone from pink to a mud brown colour, he felt the inlet and outlet pipes for the heater matrix and suggested I had a blockage and not to delay getting it checked any longer, which I did.
VW diagnostics results confirmed his suspicions and quoted £700 for the repair.

My questions for those in the know are:-
1. How common is it for a 4 yr old vehicle with just 40,000 miles to develop this problem.
2. Is it possible/probable that something was done during the replacement of the water pump that could cause this.
And if so.....
3. Is there any way of proving this.

Cheers guys (and gals.)