In fifth edition D&D when creating a bard it says you have 3 skills of your choice. I'm guessing that mean proficiency in those skills. When you level up to level 3, it you choose College of Lore, you get proficiency in 3 skills of your choice. Is that another three?
Yup, upon joining the college of lore you gain proficiency in another 3 skills. Bards are very versatile.
You can have at least 8 skill proficiencies when you pick that College.
And possibly a few more.
College of Lore gets a lot of skill proficiencies
When you pick the College of Lore at 3rd level, you can have eight proficiencies. (This is the basic amount, more later depending upon other choices).
3 for choosing a bard at first level, 2 from your background, 3 additional skill proficiencies are granted to you when you choose that archetype (College of Lore) at 3rd level.
Your first three come from the "class features" section under Bard in the PHB.
Weapons: Simple weapons, hand crossbows, longswords, rapiers, shortswords
Tools: Three musical instruments of your choice
Saving Throws: Dexterity, Charisma
Skills: Choose any three
Your second two come from your background. I'll use Charlatan as an example, which provides proficiency in Sleight of Hand and Deception.
At third level, when you choose your Bard College, you get 3 more.
When you join the College of Lore at 3rd level, you gain proficiency with three skills of your choice.
Also note that any bard at 3rd level gets the following good deal.
At 3rd level, choose two of your skill proficiencies. Your proficiency bonus is doubled for any ability check you make that uses either of the chosen proficiencies.
To really pile it on: if you had chosen half-elf as your player race, you'd have two additional proficiencies from that choice alone. Under Half-elf traits is included...
You gain proficiency in two skills of your choice.
That's 10 already at third level. If you later take the Skilled feat, you add three more. That's 13.
Another approach is to select the Variant Human at first level, which grants another skill, and as your feat choose Skilled, which adds three more.
That gets you 12 skill proficiencies at level 3. That half elf would need to wait until fourth level to get the additional three with the skilled feat for 13.
Note that you also have three tool proficiencies for the three musical instruments you choose when you begin as a bard at first level. That's a tool proficiency, which is slightly different from skill proficiency.
On page 231 of the Dungeon Master's Guide is a section on training as a reward. This opens the door to keep on increasing the number of skills a PC is proficient in based on the available down time, the campaign, etc.
Your confusion seems to stem from the difference between Skill and Skill Proficiency. Anyone can use a Skill and attempt to remember lore (History), detect traps (Perception), hide (Stealth), and etc. but not everyone is proficient in a skill.
Here is the possibilities of Skill Proficiencies at different levels for a College of Lore Bard.
At 1st level
Race - 1, Elf; 1 Human Variant (possibly 3 more if you pick the Skilled Feat); 2 Half-elf; 1 Half-Orc;
Background - 2
Class - 3
At 1st-level, you can possibly get a maximum of 9 Skill Proficiencies.
At 2nd-level, you get Jack of All Trades, which isn't exactly a Proficiency but it's still worth mentioning.
College of Lore Feature - 3
So, at 3rd-level you have a possible maximum of 12 skills if you picked the Human variant as a race and the Skilled Feat.