This paper is interested in independent sets (or equivalently, cliques) in uniform random cographs. We also study their permutation analogs, namely, increasing subsequences in uniform random separable permutations. First, we prove that, with high probability as $n$ gets large, the largest independent set in a uniform random cograph with $n$ vertices has size $o(n)$. This answers a question of Kang, McDiarmid, Reed and Scott. Using the connection between graphs and permutations via inversion graphs, we also give a similar result for the longest increasing subsequence in separable permutations. These results are proved using the self-similarity of the Brownian limits of random cographs and random separable permutations, and actually apply more generally to all families of graphs and permutations with the same limit. Second, and unexpectedly given the above results, we show that for $\beta >0$ sufficiently small, the expected number of independent sets of size $\beta n$ in a uniform random cograph with $n$ vertices grows exponentially fast with $n$. We also prove a permutation analog of this result. This time the proofs rely on singularity analysis of the associated bivariate generating functions.