Oh, and before I forget, the previous item_ entities I put *does* show. 

In the console type: developer 1

then load your map and check the console to check for any error messages pertaining to these entities, and post the results here. 

Four "Bonus item fell out of world" and a single monster appeared in the wall.

Well, in TrenchBroom at least it says the items are right there where they should so idk ._. 

Bookmark or save this, which explains error messages:
http://web.comhem.se/bjp/tooltips.txt

"walkmonster in wall at: x y z"
"Bonus item fell out of level at x y z"

This console warning is caused by having objects (monsters, weapons, ammo etc) too close to or even partly inside solid walls. The objects may also not be too close to each other, make sure their bounding boxes are separated...

Does that account for all the missing ents, or were there more? 

While those entities may not be beside other brushes, they may be overlapping with the floor. Raise the problematic entities by 8 units or so (Don't worry, the player won't know the difference!). 

I think TB (Only one I used) has incorrect Bboxes for some entities such as Quad damage and other artifacts.

Try to compensate for a powerup entity as the size of the player's bounding box. I think you may be confused because the Bbox is smaller than what the game actually thinks it is.

I ran into this problem when I was making my first few maps. 

That's gotta be a problem with the def/fgd file then right? 

Yeah, I didn't want to triple post when I caught my mistype. I think the default supplied quake defs/fgd may have the incorrect size. I remember my Quad damage having a Bbox the size of the Quad itself (quite small) when in reality the guy wants a damn auditorium to be happy! 

So fart the only items that seem to disappear are the Ring of Shadows and the Invulnerability in GUSE1M1, though it seems OK in TrenchBroom 2: https://www.dropbox.com/s/1xps9uadk8vqkgh/guse1m1.map?raw=1 

Took a quick look at your map.

Looks like the Ring of Shadows might a bit too close to the surrounding walls. To test, just place a ring out in the open before the secret door.

As for the pentagram, I can see why that is confusing as it looks like it has plenty of room. First thing to try is raise it...just raise to the middle of the room (don't move the light) it will drop down to the first solid brush it encounters. I am thinking it is too close to the floor. 

I moved both the pentagram to the ceiling and the ring to outside the secret walkway, but none appear yet :(

Can you still identify the other bonus items that fall off the level? I can't find out any other items that disappear. 

If nothing is solved, I'll load the map into my game when I get home.

As for the pentagram, if you moved it pressed to the ceiling then that could impose the same damage as having it pressed on the floor. Try the middle of the room...so there is plenty of space. 

All items have a bbox size of 32*32*64 - just like the player and the small monsters. Needs to be at least four units away from walls and ceilings! 

Height is 56 units. 

Using the metrics kegke shared, I could have both the Penta and the Ring showing. Thank you very much! :)

PS(Offtopic): I only wish the Scragg had a melee animation by spiking the player with it's spikes, and if the player is behind it, poisoning him with the tail/whatever it's called.

Don't care with this Offtopic if you don't want to :) 

Type "developer 1" in the console before loading the map. Then you'll see warning messages (along with coordinates) if items fall out of the map or monsters are stuck inside geometry. 

But, what did you guys think of the map? 

I like the effect of the dirty water flowing down the cracked floor.

To have the message about exiting not cut off add "\n" in your message to start a new line.

Keep developing concepts and general design...you are heading in the right direction! 

I guess it's because I have a bit of previous mapping experience with UnrealEd (failed due to BSP errors, which Quake doesn't has) and Doom. 

Welp, the story is as follows.

I decided to continue GUSE1M1 with the map GUSE1M2 (dur) ( https://www.dropbox.com/s/y35owf8qtxvlavk/guse1m2.map?raw=1 ) (what do you think?) but the secret cage opened by the button near the megahealth secret and the Shambler trap and bridge activated by snagging the Super Nailgun aren't really working! 

There is a super shot gun inside a cage (func_door. The cage is larger than the SSG bounding box by 12 units and is raised by using a button.

I have verified that the positioning of both cage and gun is what I think it is by turning on bounding boxes in the game.

The player is able to pick up the gun without raising the cage.

Any idea what is causing this weirdness? 

For the SNG door.

Without actually running the map, it looks like the angled door has an angle of 0. Make sure to give it an angle of 360.

Also if you want the "doors" to stay open forever, just set the wait key to a value of -1 as opposed to the Toggle spawnflag.

I honestly do not know if you can have a delay key on an item. But typically you have the sng target a trigger_relay which definitely can make use of the delay key.

As for the button:

It has a target of "secret1" but nothing has a targetname of "secret1". If you are trying to prompt that a secret was found when pressing the button then simply give your trigger_secret a targetname of "secret1".

Also make sure to set the angle for the button (360 for 0) and give it a wait value of -1 if you do not want it pressed only once.

This should help ya out. 

The SNG trap's angled brush is actually a bridge so the Shambler can smash the player after getting close quickly.

However the door is angle -1 which I believe goes up.

The trigger_relay entity is that should have the targetname "secret1". Thanks!

I'll change Toggle doors by wait "-1" and remove the trigger once.

And as for the SNG trap relay, I don't need it, and items *do* have delay time, but thanks :) 

I really don't think I ever knew items had a delay key haha.

Is everything working now?

Another fun idea to try is instead of moving an angled door for the Shambler to come across, you can have him jump over the gap to the player via a trigger_monsterjump. Just draw a brush infront of the shambler and use the height + speed keys to find what works for you. You can also set angles x y to have him go at a diagonal. 

If the player is picking up the shotgun through the cage (by hugging the cage wall I presume?) then I guess it's just a bit too close. I see you verified bounding boxes but a thing to try is expand the cage by a little and see if you get the desired effect.