Some simple problems that have lower bounds greater than the size of their inputs, are algorithms that have output sizes greater than their input sizes.
Some examples:
- The problem of listing all solutions to 3-SAT, or similarly, the problem of listing all Hamiltonian cycles. These problems both have exponential number of solutions in the worst case. Thus they have a lower bound of $\Omega (c^n),c>1$. Interestingly however, the 3-SAT problem itself has no known super-linear (greater than $\Omega (n)$) bounds! This means we do not know if it is harder than linear!
- You can even make up new algorithms like this: "completing a graph" that is, given $G = V,E$, where $E=\varnothing$, and $n=|V|$, the algorithm will output a graph $G' = V,E'$, where $E'=\left\{u,v|u\neq v\space\wedge\space u,v\in V \right\}$.
Furthermore, you might be able to compose a problem that has $\Omega (n^2)$-sized outputs, with a problem that takes $\Omega (n^2)$ as input, and outputs $\Omega (n)$ or even $\Omega (1)$-sized outputs (for example, something that counts the number outputs) to obtain a problem that takes $\Omega(n)$-sized input, and outputs $\Omega (n)$-sized output, and yet has a running time greater than $\Omega (n)$. However it might be very difficult to prove (that there is no shortcut to obtain the answer in less time).
Another way some problems have known lower bounds, is to restrict the model of computation.
Though comparison sort's lower bound does not exceed $\Omega (n\log n)$, I think its worth discussing. Comparison sort is also a problem that has a greater lower bound than its input size, but it's lower bound does not exceed $\Omega (n\log n)$, and in . However, as I was researching this, I found this question on mathoverflow: Super-linear time complexity lower bounds for any natural problem in NP. Further examples listed in the answer there are far below $\Omega (n\log n)$. I think the gist of it is, if you restrict the model of computation, you can get lower bounds for problems for which we otherwise do not have them. And if you do not restrict the model of computation, it is very difficult to prove lower bounds on problems.