Spiders! Why'd it have to be spiders?
During the first mission, Malcolm is captured by spiders. He says "Spiders! Why'd it have to be spiders?" and later "Spiders. I HATE SPIDERS!" Indiana Jones said the same thing, but about snakes rather than spiders, in Raiders of the Lost Ark. The spider scene also references the fact that sidekicks in the Indiana Jones films end up having creepy crawly creatures on them at some point during the adventure.
Later, in the first "Calendar of the Sun" mission with Indiana Jones, Indy actually says his lines from the films "Snakes! Why'd if have to be snakes?" and "I hate snakes!"