Thanks for the suggestions. Yes the hot water was probably the problem! I've added it after doing three pulls though so most mescaline should have been extracted by that point.
I shook the funnel vigorously for a minute. Please note I did this backsalting extraction several times in the past and I know it takes some shaking, but gentle shaking, swirling and inversions are enough. This time I shook a lot and no change occurred.
As for the indicator, this is not a problem. Note that although it is an irritant in macroscopic quantities, only about 0.1 ml of 0.2% solution is used, that is about 200 micrograms in the whole batch.
...and I do the dry acetone washes anyway, this removes both excess acid and the indicator as well.