This is my first game, so I'm still learning the ropes, but after a bit of googling, I think that I may of stumbled upon a bug.

I'm not a fan of the Qvefoz Hive, but unfortunately for me, they became subservient to the Pakari Mediators; some pretty advanced race. I don't have any issues with the Pakari, but I'm quite keen on dealing with the Qvefoz. Unfortunately because of the arrangement, declaring war on the Qvefoz also declares war on the Pakari...oh well.

In any case my fleet is pretty hefty now, so I decided to take on both. I was getting pretty close to capturing every single planet (I learned that captured systems have 4-pointy spears on their icons, so those that are missing them and are not my own are filled with planets).

1st bug?:
All of a sudden, I was forced to make peace with no warning whatsoever...all that work gone (142 systems). Apparently I discovered this was a bug, since on reloading an earlier save (6 months prior), I got a 24 month war weariness countdown after those 6 months elapsed rather than the immediate ending of the war.

2nd bug?:
100% Occupation (26 planets taken), 10 belong to the Pakari & 16 belong to Qvefoz, according to the contacts screen, but unfortunately as you can see from the attached image, I can't do anything other than claim the planets I bought using influence (why do I need influence to buy systems when I already own and occupy all of those systems?)

Of course perhaps I'm misunderstanding something (maybe some option that is hidden that allows me to capture the entire civilization without spending precious influence?).

I'm likely going to have to accept that I'll have to do war properly (declare war on the Pakari...sorry guys, but after capturing 142 systems and having to cede control of them I'm not going to be very nice....I'll be drooling at the "10 year "Truce" counter).

There are some other bugs as well I noticed:
-Domesticated Prethoryn has a few bugs (can't disband the unit (well I learned I could disband the individual components of the fleet, and once it had zero ships in it, then I could delete it) and the visuals are a bit messed up see pic).

-"Command Center" on my star bases says it adds +10% to fire speed, but it appears to add +20% (went from 70% -> 90%).

-Automated sectors building colony ships when there are no planets to colonize (maybe by design, make it faster if you come across a planet later). For that matter, how do you regain control of sector built ships? (blue icons), I tried dissolving the entire sector, but the ship still remained blue and unselectable.

Loving this game still, but a lot of time went into capturing this territory...fingers crossed I can do so when declaring war on the Pakari next.

Occupied system doesn't meant you will get it after the war ends. Only occupied and claimed system that will be yours after the war ends. Reagarding your screenshoot, you already at victory, click achieve war goal button with green tick and force your victory by clicking send offer button.

Influence is extremely precious and purchasing 142 systems with influence will require at the least 30*142 = 4260 influence. If I spend my influence on nothing but claims, it will take 59 years (@ +6 influence/month) of in game time to defeat them...surely there is some easier way to defeat an opponent?

Back to my current game:

10 years later and I declared war on the Pakari and was able to use some goal along the lines of "annihilation", so every system I captured immediately became mine...I'm guessing it may have something to do with being an ancient race, but apart from their terrible decision of offering protection to my most hated enemy, they were pretty decent fellows.

After defeating them, the Pakari disappeared from the game, but I inherited their vassals...the ones I actually want to destroy, argh!, so I granted them independence and have to wait another 10 years before I can declare war on them.

Edit:Claims I think start at about 30 for me (due to other reductions), so I fixed that....

If you want to destroy your vassal you can assimilate them, talk to qvefoz hive your vassal then find assimilate option, there are some requirement to do that but you'll find what the requirement is in the button tooltip.

Regarding your first question the easier way to take over your enemies is make them your vassal then assimilate them, or built colossus which is only available if you have apocalypse dlc then declare total war which is an 'annihilation' war goal to normal empire.
Here are some information about war goal:
https://stellaris.paradoxwikis.com/Warfare#Casus_Belli_and_Wargoals

Thank you for the information and the provided link.

I did try playing around with the Vassalize Casus Belli on another race, and found on an earlier save I could get the dialogue option to get the Vassalize Casus Belli, but on this most recent save I cannot.

It looks like the reason is because they are currently at war with another race, is that why I can't get the option to ask them to become a Vassal?

Your welcome. Hover your mouse on vassalize button, the tooltip should tell you why you can't ask them to become a vassal.

With a bit more education, I'm fairly convinced that there were no war bugs responsible, and it was user error :)

So I've learned a few things since:

-Conquest wars (claiming land) I think ends automatically when the claims for you, your vassals, and Federation members are fulfilled. This might explain why I received the message of "forced peace" in the case of the "First bug" without the war weariness prompt, perhaps I just missed conquering the planet/system I needed to fulfill those objectives, or I might of added another claim after reloading it.

-For bigger vassals, integration is a bit of a waste of time. I tried to integrate a large vassal at a then current 4505 influence (900 months), and after spending 2685 influence points (about 45 years worth), I discovered that it had increased to 6285 influence.

Still very much enjoying my first game (certainly love the depth and detail and how much fun it was to learn all of these mechanics), although I don't see a way to end the game and get a score or summary anywhere. Earlier on I did manage to trigger one of the victory conditions but opted to continue on (Domination I think). I have both the requirements of Domination Victory and Federation Victory fulfilled...so is there anyway to end the game and get a score summary?

As far as i know there are no way to end the game after you skip your first victory screen.

Thanks for the quick answer, after a bit of time googling, it seems this is the case.

Oh well, nearly hit year 3000...I'll continue on a little longer...