Although the Akademia Vortaro suggests the word anomalio, adopted since the Dua Oficiala Aldono, I see no mention of this word in the Baza Radikaro Oficiala nor in the website La bona lingvo. I study health sciences, so I am more often exposed to the word anomaly than the general population, but in spite of that I do not think it is such a rare word in everyday life too. So shouldn't we be able to express the same idea with more common morphemes?
"Anomalio" can be found in PIV. (http://vortaro.net/#anomalio)
"Escepto" and "Eksternormalajxo" are also mentioned there. Otherwise I would suggest "nenormalajxo" or even "malnormalajxo".
If anomalio is in the Akademia Vortaro, I wouldn't doubt that it's usage is valid. However, I also understand your hesitation to use words that may not be readily understandable. I suggest nenormalaĵo as opposed to malnormala. Althought it is true that the two differ semantically in that nenormala is "not normal" and malnormala is "opposite of normal", in practice they seem to be the same. However, in every search, nenormala / nenormalaĵo is more common than malnormala / malnormalaĵo.
Searching on Google:
- nenormalaĵo trafficked 3,330 results, while malnormalaĵo trafficked 2,450
- nenormala trafficked 15,800 results, while malnormala trafficked only 5,680
Searching on Tekstaro:
- Neither nenormalaĵo nor malnormalaĵo trafficked any results in Tekstaro, which only indicates that it hasn't been used in the tracked literature.
- However nenormala trafficked 17 results, while malnormala trafficked only 3
This demonstrates that nenormala and nenormalaĵo are at least in mild use, and considering that anomaly is a synonym for irregularity or abnormality, and that the Greek word it is derived from has the same meaning, I'd concede that anomalio could be ceded to nenormalaĵo.