كَانَ زَيْدٌ فِي الْمَدْرَسَةِ
Translation: Zayd was at school.
كَانَ: past incomplete verb; زَيْدٌ: nominative ism.
فِي: preposition; الْمَدْرَسَةِ: genitive noun.
The phrase فِي الْمَدْرَسَةِ relates to an understood accusative predicate of kāna.
A predicate can occupy an accusative syntactic role without every word in its phrase showing fatḥa.