since el capitan some pages documents are in code

DId these documents use a custom font that is not installed in El Capitan?

I should have asked this up front. What explicit version of Pages (About Pages) are you using?

There is no guarantee that the following will correct the Palatino font corruption — that I cannot reproduce here on El Capitan with Pages v5.5.3.

Boot into Safe Boot mode. This is rebuild your system font database and your local user font database. Updating to El Capitan did not do the latter.

1. Shut your MacBook AIr down. Connect it to the electrical outlet. Don't do the following on battery.
2. Press the power button, and immediately press and hold the Shift key — until you see the horizontal progress bar. This will be slower than usual.
3. You will arrive at a login screen, and Safe Boot mode will be indicated in the upper-right portion of the screen.
4. After you enter your password, but before you press the right-facing arrow to sign-in, press and hold the shift key again until all of your Desktop icons have repainted. Things will be slower because drivers purposely were not loaded.
5. In the Finder, press shift+command+G. This is the Go to Folder dialog. Copy and paste the following into that text field, and then type Go.
   ~/Library/Caches
6. You are now inside the Caches folder located in your own Library folder. This is where your running applications write their temporary information, and it is safe to remove the contents of this Caches folder. This is a trouble-shooting effort, and normally you won't need to do this.
   1. Select all (command+A) inside this Library/Caches folder.
   2. Right-click on any selected icon inside this Caches folder, and choose Move to Trash.
   3. Skip emptying your Trash for now.
7. Reboot normally. Now, you can empty your Trash.
8. See if the font corruption in Pages v5.5.3 has cleared up.
   

I had the same problem and tried a different font in Pages and solved problem.

Anne,

I was hoping that the Safe Boot would clear some things up. There is a shorter set of steps to just rebuild the user font database, but it would involve use of the Terminal, and now we know it is not font cache corruption anyway.

You have the latest version of Pages (5.5.3) on El Capitan. Removing and reinstalling it likely will not change anything.

If you open Font Book (Launchpad : Other : Font Book), and you select the ⓘ symbol from the Toolbar for your selected font that is creating the jibberish — what kind of font does it report, and in the Location field, what is the extension on the font name?

Also, here is a link about Font management in OS X by another community member.

Oh, that capricious Palatino. Glad it decided to work for you.