It all depends on the alternative!
In a vacuum, there's nothing wrong with doing a second internship at the same company. I not only did two internships at the same place (one in highschool, one in college) but also did a co-op there as well.
However, there are some things to keep in mind:
What would you be doing if you didn't apply? If the answer is "not work at an internship", then, yeah, taking the internship is almost surely the right answer.
But if the answer is, "Apply elsewhere, find a different one"... then it gets a bit trickier. Even though the specific job/department is changing in this second internship you're asking about, it's still at the same company. Which means the skills you're learning for this second internship might be a bit less varied.
Are you going to lose out on experience?
Similar to the first... if taking this internship is replacing finding a different place to work: what about the variance of experience you're getting? One reason a lot of IT people shift jobs quite a bit isn't just the pay - but the skillset. If you stay in one job for a long time, you're likely not improving your skillset as much as if you were finding new things and learning new technologies. But it's the same thing with business environments: working for a completely separate company will give you a better perspective of the business world - you'll have two places to compare/contrast instead of just one data point.
This isn't to say "Don't take the internship". Because taking it definitely is NOT a bad thing. It's more to say... weigh it against what the alternative is (which none of us here know what that is.)