Hi, I just leveled my tempest cleric Lumi to level 3 and when I go to select my spells, I have 2nd level spells available to view, but both of my available slots are taken automatically by the tempest domain spells, shatter and gust of wind. The rest of the spells have the button to prepare them but it is greyed out like I have selected my max amount of spells. The first level spells worked properly and I haven't had an issue all through levels 1 and 2. 

https://www.dndbeyond.com/characters/72610942

You are confusing Spell Slots with Prepared Spells. Prepared spells are how many spells you can prepare each day, Spell Slots are how many spells you can cast each day of various levels.

https://www.dndbeyond.com/classes/cleric#Spellcasting-108

Preparing and Casting Spells

The Cleric table shows how many spell slots you have to cast your cleric spells of 1st level and higher. To cast one of these spells, you must expend a slot of the spell’s level or higher. You regain all expended spell slots when you finish a long rest.

You prepare the list of cleric spells that are available for you to cast, choosing from the cleric spell list. When you do so, choose a number of cleric spells equal to your Wisdom modifier + your cleric level (minimum of one spell). The spells must be of a level for which you have spell slots.

For example, if you are a 3rd-level cleric, you have four 1st-level and two 2nd-level spell slots. With a Wisdom of 16, your list of prepared spells can include six spells of 1st or 2nd level, in any combination. If you prepare the 1st-level spell cure wounds, you can cast it using a 1st-level or 2nd-level slot. Casting the spell doesn’t remove it from your list of prepared spells.

You can change your list of prepared spells when you finish a long rest. Preparing a new list of cleric spells requires time spent in prayer and meditation: at least 1 minute per spell level for each spell on your list.

I hope that helps.