I'm trying to create a homebrew subclass and at level three they gain a feature that lets them choose one of four cantrips, at later levels(3,6,11,17) they will be able to choose another spell. I have got it working but they are given all the choices at third level but don't get the spells until the level they should. Is there any way I can make it so that they don't get the choice for the other cantrips until they reach that level? 

Sidenote they can also take one cantrip muliple times any tips for this?

Unfortunately not, no. There’s no real way to address either of those two issues.

Damn, well I'll just live with it then. Thanks alot (for all your guides and stuff)

 Ohh and if you see this, do you know if there's a way to change how many spells/cantrips a subclass learns

Not through normal spell progression. You can add a new subclass feature: "Bonus Spell" and add that class's spells and spell level(s) as a choices in that feature.

Yeah I didn't think it was as easily implemented as i hoped, but thanks none the less.

It's near the same as a bard's Magical Secrets. Just give them 1 choice and say the spell doesn't count against spells known.

It is a lot more cumbersome for a prepared caster though, as the player would have to go back to the character builder to swap it out on a long rest.

If you don't mind me asking, why is the first issue not resolvable within a single feature? I was able to give different spells at different levels, so why is it that giving the same option for spells at multiple levels just causes the builder to offer the choice from each level at lower levels than they should appear?

Edit: Doing some testing and I've found an odd discovery. So far, granting a cantrip and a level 1 spell at level 3, then a level 2 spell at level 5, level 3 spell at level 9, level 4 spell at level 13, and level 5 spell at level 17 works.

But granting a choice of cantrips at different levels doesn't seem to work. The choice for every cantrip is offered even when some cantrips are set to require a higher character level. What's going on that makes this not work? 

Edit 2: Granting 2 of the same choice of cantrips at level 3, and then 1 of 2 1st level spells at level 5 is also broken. The choice at level 5 appears at level 3 in the builder.

Edit 3: Granting a single spell (no choice) at different levels seems to work correctly.

Edit 4: Granting a choice of spells and then no-choice spells at different levels seems to work fine. But more than 1 choice of spells seems to utterly break it. Maybe the only way is to just have a new feature for each choice of spells. 

The odd thing about when I tried to use the Class Feature Options tab is that spell choices granted this way seemed to include spells I didn't want to include. It somehow included all my homebrew spells, despite me not entering them into the spell list.

Whenever you create a feature at a lower level that offers a single spell at any level the system works just fine.

Whenever you create a feature at a lower level that offers a choice of spells at that level, the system works just fine.

Whenever you create a feature at a lower level that offers a choice of spells at any higher level, the system will display all choices in the builder at that lower level, but not actually grant the chosen spell until the designated level.

That’s just the way the system seems to work. Why? I dunno. I don’t work here, I just live here.

Quote from Hakase25 >>

The odd thing about when I tried to use the Class Feature Options tab is that spell choices granted this way seemed to include spells I didn't want to include. It somehow included all my homebrew spells, despite me not entering them into the spell list.

 
When you added the spells, how exactly did you fill out the form? What precisely did you enter into the different fields and select from the different dropdowns?

I entered:

• SPELL (the one that accepts specific spells by name) > Gust, Mold Earth, Control Flames, Dancing Lights, and Shape Water
• ABILITY SCORE > Wisdom
• COUNTS AS KNOWN SPELL > No
• AVAILABLE AT CHARACTER LEVEL > 5

And touched nothing else. When I entered the character builder, the choices included the cantrips mentioned, but also included all the homebrew spells in my homebrew collection.

Quote from Hakase25 >>

I entered:

• SPELL (the one that accepts specific spells by name) > Gust, Mold Earth, Control Flames, Dancing Lights, and Shape Water
• ABILITY SCORE > Wisdom
• COUNTS AS KNOWN SPELL > No
• AVAILABLE AT CHARACTER LEVEL > 5

And touched nothing else. When I entered the character builder, the choices included the cantrips mentioned, but also included all the homebrew spells in my homebrew collection.

 
Odd. It really shouldn’t. Did you list that subclass in the list of classes attached to the character?

What do you mean by "list that subclass in the list of classes attached to the character?" The character is a level 5 rogue, no multiclass. Not sure if there's anything else beyond that for choosing subclasses in the character builder.

You said they were Homebrew spells. Right? You know how you have to designate which classes can use the spell when you created one?

Did you give that subclass the Spellcasting feature? If so, did you add this subclass to the list of classes that can cast those spells?

If not, when you added the spells to the subclass, did you (intentionally or otherwise) select a class from the “Spell Class” field in addition to just adding those spells by name to the “Spell” field?