入る and 入れる: enter, put in, and be included
Compare a person or object entering with someone putting an object inside. Apply the pair to spaces, capacity, ingredients, groups, and schedules.
Enter a destination or put something inside
入る marks a destination with に when a person or thing moves into a space. 靴を脱いで部屋に入りました。 says that the person took off their shoes and entered the room.
入れる marks the item being put inside with を and its destination with に. 読み終わった本を棚に入れました。 clearly separates 本を from 棚に.
Capacity and included ingredients
この瓶には水が一リットル入ります。 describes the bottle's capacity. An ingredient already present can be expressed as スープに野菜が入っています。 Here, が marks what is included.
An ingredient being added takes を with 入れる. 紅茶にレモンを入れます。 marks the tea as the destination with に and the lemon being added with を.
Joining groups and adding schedules
入る also describes becoming a member of a group. 来月から写真部に入ります。 says that the speaker will join the photography club next month.
明日の午後に予約が入りました。 says that a reservation was added for tomorrow afternoon. If the speaker records a schedule, use 予定をカレンダーに入れました。 Distinguish a reservation appearing from someone entering an item.
Quick check: How do you describe lemon already being in the tea and the action of adding lemon?
Show the answer and why
For the state, say 紅茶にレモンが入っています。 For the action, say 紅茶にレモンを入れます。 What is included takes が, while what someone puts in takes を.