i'm afraid i side with the bbc on this one. i worked in the design industry for 12 years (and am now freelance doing the same) designing cross stitch and tapestry kits. the company i worked for used a lot of licensed brands, forever friends, beatrix potter etc, all of which were under contract and had to be paid for with a yearly sum plus a percentage of sales.
the doctor who franchise will fall under the same rules, any product using it eg, clothing, lunch boxes, toys etc, will all have to have gone through the same process.
there is nothing to stop anyone making a toy like this for themselves or their own child, but the fact that she is distributing the pattern is what the bbc have cottoned on to. all she has done is translated an initial idea into a knitting pattern, but the initial ideas were not hers to use. they were the work of the doctor who writers, design and costume department, so she has infringed on their copyright.
tbh, i don't think it's a money issue, it's more to do with having control over the merchandise quality. i say this as i know someone who works on doctor who in special effects, and also after having has my own designs copied and found someone selling them on as their own work