I suspect that it is because I collected the resources first when infrastructure wasn't upgraded and now it's only giving me 1 crate for science and mining.
Infrastructure was upgraded after I collected resources
Day 2 gave me 1 crate from science and mining
Day 3 is also just giving me 1 crate from science and mining
System also gives 1 con ticket, but it's max out at lvl1 so it's not relevant