One common theme could be betrayal. Alec might be in a situation where he has to betray Clary for some reason, like loyalty to his own group or family, which causes her harm.
Love triangles can also be a theme. Maybe Alec is involved with someone else while having complicated feelings for Clary, and this leads to him hurting her in the process of sorting out his emotions.
Friendship is a very common theme. They are both important characters in the Shadowhunter universe, and many fanfictions explore how they become friends and support each other.
A theme that also pops up is the discovery of new sides of each other. Clary and Alec each have their own personalities and secrets. Fanfictions often explore how they learn more about each other, which in turn strengthens their bond. For example, Alec might discover a more vulnerable side of Clary, and vice versa.
One common theme is the adjustment of their relationship. With the pregnancy, they need to redefine their roles and how they interact. Another theme is the support from their friends and family. In many fanfictions, their friends play an important part in helping them through this new chapter.
Love and commitment are common themes. Their marriage is a new chapter, and fanfictions often explore how they stay committed to each other in the face of various difficulties.
One common theme is redemption. Jace usually has to atone for his actions that hurt Clary. For example, he might go on a quest to find a way to reverse the damage he's done.
One common theme is friendship. Many fanfics explore the deepening of the friendship between Alec and other characters. For example, how Alec and Clary become closer friends over time and support each other through various difficulties.
One common theme is family. Since they both have complex family backgrounds in the Shadowhunter world, their married life often involves dealing with family issues. For example, how their families interact with each other.
There's a fanfic titled 'Broken Bonds' which focuses on Clary's hasty decisions that deeply wound Alec emotionally. The story delves into Alec's inner turmoil as he tries to come to terms with Clary's actions. It's a great read if you like exploring complex relationships in fanfiction.
One place to start looking for Alec Hurts Clary fanfiction could be Archive of Our Own (AO3). There are a large number of fan - created works there. You can search using the relevant tags and keywords to find stories that focus on this particular scenario.
Well, one common theme could be the exploration of their relationship in more intimate or romantic settings. Another might be the development of their characters within those scenarios.