In create mode on PS3 my bags are lacking some of the LBP3 content like the physics tweaker and power-up pedestal etc etc. 
(Advanced content is already on and I have completed the tutorials).
If anyone has a way to solve this issue that would be great!
Thanks!

Try the Popit Academy.

I've done the entire poppet academy since they're in the tutorials!

Hmm... I'm not certain where you get those tools, or if they just come by default. I'm pretty sure it's just a result of turning on Advanced Create Mode. At least, that's why my Google search is telling me. Are you sure it's on and you're looking for it in the right category?

Yeah I've turned adv. content on and off multiple times and checked the entirety of both the goodie and tool bag, I thought it would be because I am on PS3 but I have nothing to compare it to.

I've searched around and nobody else seems to have/have had this issue...

Yeah, I've never heard of someone having an issue with getting Tools Bag contents, at least with LBP3.  Perhaps try contacting StevenI? If anyone will be able to figure out what the problem is, it's him.

Will do, thanks!

Well, I did have that problem. It was because I used backed up profile from LBP2 in LBP3. I wanted to because I used to have older PS3 which have had laser problem since I started playing Uncharted 3, so I couldn't run the game, but in my friend's PS3. While the fix was easy to do (play LBP2 and import profile from there and THEN launch LBP3 after deleted LBP3 profile (which had that issue), I couldn't do that because my friend never played this game on his PS3 so there's no patches and it'd take hours to download them all. This problem has been eliminated when my mum bought me a new PS3, where I was able to do that.

So my suggestion:
If you do have LBP3 data saved with LBP2 data imported from the backup. Then to fix it you need to delete LBP3 profile data from Game Data Utility. This will delete all of your collected stuff: your levels in your moon, costumes, stickers, objects, collected prize bubbles from Popit Puzzles, Adventure and DLC level packs. So if you still have collected or made stuff in LBP3 and you don't want to lose it, follow the GlitchMaster7's video here: http://youtu.be/Ngqq5dXJ9fc Even if he's doing that on LBP2 and recovering stuff in PS4 version of LBP3, don't worry it's the similar process. You can skip the DLC part because you have it on PS3 already (if you bought so). So if you're sure you have saved everything possible, delete the data, go launch LBP2 (to make LBP3 verify that you played previous game before and enable you option to import data when starting the game). After you successfully appeared in pod quit the game and launch LBP3. If done correctly you should see a message pop up that you've played LBP2 before and shows you can import the data. Import it and you will have your old stuff back and to recover rest of your stuff you just do exactly what GlitchMaster does in PS4 in the video. Bear in mind that you also lost the prizes collected from DLC level packs, adventure and popit puzzles. If you don't really want to play each level again to collect the stuff back you can play Time-saver pack levels from ex. Smuffy04. If your also about getting adventure stuff you can send me an friend invite (kubac2000) and we will play my back up levels

But if you haven't played LBP2: Do the same thing except going to LBP2.