Does it sound too redundant to use "Rare anomalies" in a sentence to describe a rare occurance?
Anomaly simply means
something that deviates from what is standard, normal, or expected: there are a number of anomalies in the present system
It does not encompass the connotation of rare, just something that deviates from what is standard. Hence, it is alright to use 'rare anomalies'. Or, if you don't feel comfortable, you could just use another phrase like 'rare occurrence'.