Unlike C-3PO, R2-D2's memory was not wiped at the end of Star Wars: Revenge of the Sith. This means that all of his memories are intact, including his memory of the first time he traveled to Dagobah. During the sixth season of Star Wars: The Clone Wars, Yoda embarks on a quest to learn how to preserve his consciousness after death. Yoda takes R2-D2 along to help fly the ship, but in the process, R2-D2 gets a tour of many important locations that are strong in the Force. However, even though this tour includes the Sith homeworld, R2-D2 seems to dislike Dagobah the most because of the unfavorable terrain and the general foreboding aura of the planet.
Yoda and R2-D2's journey begins in "Voices" after the spirit of Qui-Gon Jinn contacts Yoda and directs him to Dagobah to learn more about communicating after death. When Yoda and R2-D2 arrive on Dagobah, R2-D2 makes his distaste for the planet clear. After Yoda leaves the ship, R2-D2 gives some inquisitive beeps. Yoda responds, "Yes, stay with the ship, you may. This task, for me alone it is." This statement implies that R2-D2 asked to stay behind rather than venture forth on the planet.
At first, it could be assumed that R2-D2 chooses to stay with the ship because of the swampy terrain. Star Wars: The Empire Strikes Back shows the possible consequences of R2-D2 attempting to traverse Dagobah; he almost immediately sinks into the swamp. While Luke helps him clean off the worst of it, R2-D2 remains covered in mud for the rest of their time on the planet. In Star Wars: The Clone Wars, R2-D2 might simply be trying to avoid sinking or getting his gears filled with mud unnecessarily.
However, R2-D2's response after Yoda leaves shows that his reluctance to leave the ship stems from more than a desire to stay clean. R2-D2 shudders in place while whirring nervously. He also immediately asks if Yoda is okay once Yoda returns as if R2-D2 feared for Yoda's safety. Years later, Luke remarks that the planet "gives [him] the creeps," and R2-D2 might have picked up on the creepy atmosphere.
R2-D2's fear may seem out of character. After all, he normally charges off into danger to save the day. However, in most of those cases, he faces a clear objective to accomplish or an enemy to defeat. On Yoda's Force journey, R2-D2 has little information to work with and has no idea what might be lurking on the planet's surface. Thus, he reasonably remains with the ship while Yoda gathers more information.
Dagobah is only the first stop on Yoda's journey. The duo also travels to the Wellspring of Life and Moraband, the Sith homeworld. Notably, R2-D2 leaves the ship without hesitation on both of these worlds. While Yoda still asks R2-D2 to stay behind and guard the ship, R2-D2 seems much less afraid to explore. Thus, in some ways, Dagobah could be considered more frightening than Moraband to R2-D2, possibly because the dangers of Moraband are far more obvious than the hidden mysteries found on Dagobah.
Therefore, when Luke tells R2-D2 that they are traveling to Dagobah in Star Wars: The Empire Strikes Back, R2-D2 knows the exact location that Luke is talking about. R2-D2 might not have told Luke about his earlier trip precisely because R2-D2 did not leave the ship; he did not have much additional intel to provide on the planet itself. Still, this particular adventure further shows that R2-D2 holds a lot of information that he keeps to himself, including more information on the Force than most Jedi.
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