I got a 1099-R with gross distribution of $0.46. Turbotax throws an error asking for gross distribution >$1.00. What should I do?

You do not need to report it.  If it's less than $1, it would round down to zero, you do no need to report it.

Taxpayers should report nothing if total interest is 49 cents or less, or $1 if it is $0.5 to $1.49.