I'm making/made a monk with 3 levels of warlock to build a ninja. I will only ever have level 2 slots and 13 CHA (+1, very important). What 2 level 1 spells should I choose (limited to PHB)?

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I'd definitely go with Hex. Given how many attack rolls you'll be making, a per-hit damage bonus is a clear winner. For the other, I voted for Expeditious Retreat, but I almost went with Comprehend Languages because it's a good choice for a spy type. I figure Expeditious Retreat for a faster getaway might be the better choice, since you can save the Ki points by not having to use Step Of The Wind.

Hex and something for out of combat like unseen servant.

Hex is just so much better than any other option that you are going to just want to keep the other spell slot ready in combat in case you lose concentration on it.
All those unarmed strikes and hex damage is going to add up.

I'm surprised expeditious retreat is getting so many votes considering I am already a tabaxi monk and movement speed is not an issue in the slightest.

I have already accomplished running into a burning barn, searching it for people, and carrying someone out at half speed, all in a single turn.

I almost didn't included it in the poll because I was sure I wouldn't need it, but included it to be thorough.

I kind of understand why armor of agathys is getting votes, but the highest it will be cast is level 2, and I think mirror image is strictly better.

Hex is always fantastic and gives you some fun abilities out of combat if used creatively. Try hexing a King's charisma when he's giving a speech!

If you're going for Monk and you want to make him a ninja, you can't go wrong with Expeditious Retreat.

Big fan of spells like Unseen Servant.  So may uses.  Hex is good especially the skill disadvantage and really shines if your party grapples or knocks enemies prone a lot.  If you are thinking of using Hex you may want to look at an out of combat /escape spell like Servant or Expeditious Retreat due to concentration issues.  Protection from Good and Evil is great but it may compete with Hex for concentration.

I ended up voting hellish rebuke along with hex. Thought HR would be more flavor of a ninja pointing at an enemy and then taking damage. 

I don’t know if I missed it but what pact are you going with? With only 3 levels I would like Tome to pick up rituals to flesh them out. But I assume you probably did Blade. 

Quote from ThriKreenWarrior >>

I don’t know if I missed it but what pact are you going with? With only 3 levels I would like Tome to pick up rituals to flesh them out. But I assume you probably did Blade. 

 Oh, I forgot to include it, I'll edit it. I'm going pact of chain. I have a low spellcasting mod, so didn't see the point in picking up more cantrips (not a spellslinger anyway), and didn't see the point in being able to summon a weapon that does as much damage as my fist.

So I'm going with trained ninja animal idea.

I chose Hellish Rebuke and Hex.

Hex is a no-brainer, it will just add so much damage dice to your character and fits your overall theme. 

Hellish Rebuke may not stop attacks from hitting you, but it punishes them when they do, and quite painfully. When you get to level 3, you'll always cast it at 2nd level and have 2 spell slots, one for hex and one for this. 

I'm sure I am going to be using my spellslots for mirror image as much as hex in combat, so it really shouldn't be a third combat spell... (For obvious warlock reasons).

If you are a Hexblade dip I think it is Hex and Shield.  The shield spell helps alot in combat