Two questions immediately spring to mind here.
The first is, how? Granted, there's a vacuum in space and a lack of gravitational force and all that, but the pressure differential in a tank is "just" 1 atm more than it would be on the ground, where we've had pressurized hydrocarbon tanks for very, very long. I can't see gravity - or the lack thereof - affecting the process that much either. Sure, there's less pressure at the top of a tank in gravity, but also more at the bottom.
And if you go down to the molecular scale, what could possibly be going on to cause excessive boil-off? Neither the tank material or the gas/liquid would be any more prone to diffusion than on the ground. Hydrocarbons are big molecules, and tank walls are made to be vapour tight. Does the tank material age faster in space than previously assumed? If so, the ISS would have been in big trouble long before now. Are valves and flanges somehow less vapour tight in space? Again, the ISS doesn't seem perturbed by it. And there have been multiple instances of small-scale spacecraft operating fine in space for years before using their engines - and hence, their fuel - without any unexpected issues.
The second is, assuming they have found out that boil-off is worse than previously thought, how did they find that out now? I mean, they haven't conducted an experimental test of large tanks filled with fuel in space yet (small tanks have been tested and found adequate for Mars trips already, as demonstrated by the multiple spacecraft that have landed there without succumbing to boil-off problems). Any calculations, simulations, or theoretical exercises they could have run to evaluate the feasibility of orbital fuel depots, surely NASA would have also run decades ago? The discovery on hitherto unknown boil-off problems would have required SpaceX to run an unprecedented research project on the subject. In that case, I presume we would have known about it earlier.
I mean, it could be that they have discovered something new, but from existing knowledge, I don't understand what or how that could be.