Many social media systems explicitly connect individuals (e.g., Facebook or Twitter); as a result, they are the targets of most research on social networks. However, many systems do not emphasize or support explicit linking between people (e.g., Wikipedia or Reddit), and even fewer explicitly link communities. Instead, network analysis is performed through inference on implicit connections, such as co-authorship or text similarity. Depending on how inference is done and what data drove it, different networks may emerge. While correlated structures often indicate stability, in this work we demonstrate that differences, or misalignment, between inferred networks also capture interesting behavioral patterns. For example, high-text but low-author similarity often reveals communities "at war" with each other over an issue or high-author but low-text similarity can suggest community fragmentation. Because we are able to model edge direction, we also find that asymmetry in degree (in-versus-out) co-occurs with marginalized identities (subreddits related to women, people of color, LGBTQ, etc.). In this work, we provide algorithms that can identify misaligned links, network structures and communities. We then apply these techniques to Reddit to demonstrate how these algorithms can be used to decipher inter-group dynamics in social media.