A variant of the well-known Set Covering Problem is studied in this paper, where subsets of a collection have to be selected, and pairwise conflicts among subsets of items exist. The selection of each subset has a cost, and the inclusion of conflicting subsets is associated with a penalty to be paid. The problem, which can be used to model real applications, looks for a selection of subsets that cover the original collection, while minimizing the sum of covering and penalty costs. In this paper we consider a compact mixed integer linear program and we solve it with an open-source solver. Computational results on the benchmark instances commonly used in the literature of the problem are reported. The results indicate that the new approach we propose is capable of good results, both in terms of lower and upper bounds, although not matching the state-of-the-art on average. The new approach was, however, able to improve 9 best-known heuristic solutions.