Flora's tours are operated via special zodiacs and occupancy is limited to 12 by design of these boats. 12 Might feel a crowd on a small vessel to some, hopefully 20 people along 200+ feet of beach doesn't. Maybe don't be surprised if people naturally converge on a solo seal enjoying a bit of sunbathing, however!
It's not impossible to encounter the guests transported by another of Flora's zodiacs but Flora's operations are designed to help mitigate such encounters. The Ecuadorian government also requires ship operators plan and avoid concentrated, heavy footfall on the same locations day in, day out.
Most days on the Flora will offer at least two opportunities to enjoy an excursion, with up to four options for the day's activities. You'll typically sign up for your desired activity the night before and choose an available time to participate.
Certain highlights such as the Charles Darwin Research Center may mean a far higher likelihood of encountering other guests as there's only one center to visit and maybe up to half the ship could sign up for a morning visit, for example.
While on the other hand, a small fleet of zodiacs shouldn't ever really land on the same outcropping of beach or float over top of one another during a deep sea snorkelling session.