When I made my Exit-8 game (for a submission to a jam that is not mine) I made it 60-40 (60 for anomaly)... no specific reasons for those numbers just instinct I guess; but I too felt 50-50 was too low of a probability occuring.
In my head I also made two distinct categories for the anomalies: the obvious anomalies and the subtle anomalies. So, in the gameplay, the probability is more like 40% normal occurence, 30% obvious anomaly, and 30% subtle anomaly; which felt fair in my guts.
In most Exit-8 games there are also the deadly anomalies (I didn't make it for my submission back then because I didn't have enough time)
Anyway, probably there is no right answer until you try making it and getting people to test for them. Good luck!