Hello. First, no judgement but this is a big wake up call for you. Your marriage is in jeopardy due to your actions. If his mother living with you causes this kind of stress, then you need to be clear and speak with him that you can't do it. It's okay to have boundaries. You need to set them. Even if she stays, set a boundary for your home so you still feel like it's your home.
Okay, SOOOO, you are most likely not pregnant. Apps are great but they just average numbers and don't check our hormone levels or know what is going on with our body or our life. Stress is a main reason for periods being late as is change in routine. Illness, weight gain or loss also contribute. Thyroid issues or hormonal imbalance are also both big reasons for irregular cycles. but I'm going with the stress of your infidelity and guilt.
Can you see a therapist either by yourself or with your spouse to get your life back on track? And cease all communication with the man that clearly is someone you know. You should.
Anyway, don't think you are pregnant. good luck