Can 会儿 be pronounced 3rd tone?
You are right. 
会 is the 4th tone in the dictionary (the most official 新华字典) and if you are in a test, you'd better follow that. 
However, in daily Chinese, there are a lot of people using the 3rd tone as casual speech. 
Actually, 会 is a kind of popular mistake. There are a lot of examples for that. 
In the ancient book POEM （诗经；shi jing）, one sentence reads 君子好逑 jun1 zi3 hao3 qiu2. But people tend to read it as jun1 zi3 hao4 qiu2. Upper level Chinese classes in Chinese high school specifically teaches the importance of these terms. But the daily talking is in a kind of casual style. 
Anyway, people are able to follow your mind despite one or few pronunciation differences.