Some of the spaces in confluence 3.5 using the theme 'global look and feel' were working fine but after upgradation to confluence 5.1 some of the pages are broken and are not displayed properly.
What should be the reason?
There's some layout changes between 3.5 and 5.x versions of Confluence.
Please check if you have any customizations that might need to be rewritten to the new layout: https://confluence.atlassian.com/display/DOC/Changing+the+Look+and+Feel+of+Confluence
About the pages being broken, do you mean the links not working or the wiki-markups not been migrate to XHTML?
If it's a migration issue, check this approach: https://confluence.atlassian.com/display/CONF50/Migration+from+Wiki+Markup+to+XHTML-Based+Storage+Format
If the links to that pages are not working as it should, then try to Rebuild the Indexes from Scratch: https://confluence.atlassian.com/display/CONFKB/Rebuild+the+Content+Indices+from+Scratch
Hope it helps!
As Bruna mentioned, there were changes made to wiki markup in version 4. If you have pages showing an "unmigrated wiki markup" message, that could explain why. Also, if you have plugins that are not compatible with your new version of Confluence, that could also be a source of the layout issue.
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