I've been drinking Soylent since the early days. At times I've almost exclusively drank soylent. Since the first early adopters received their first shipments almost 1 year later than originally anticipated.
The one thing that has caused mild indigestion for me was when I was drinking Soylent almost exclusively in combination with energy drinks. Specifically Monster Lo-Carb (1 each morning on weekdays). Once I eliminated energy drinks from my diet the indigestion stopped.
Otherwise my personal impression (given my mostly eventless but extensive history with soylent, along with an inability of the company to precisely define the source of the issue) is that a lot of the bad press is a smear campaign.
EDIT: Another thing that has crossed my mind is that the American diet is notoriously bad. When switching diet from mostly bad to mostly good a person should expect a change of the composition of the bacteria in their stomach. Which could lead to the sensation / symptoms of indigestion.