you are interrupting the user- if he has many tabs open and you alert he suddenly is directed to your tab.. A pain in the ass for me as an user. that is the biggest concern for me..
having said that console.log does not work in all the browsers IE7 for one does not support the same.
well using alert is fine so long as it is clear why there is an alert.
also alert is not helpful to log JS objects you can only display strings.