It looks like you have enabled "series items" on your document library, are the site running on Meeting Forum template?
Share List Items Across All Meetings (Series Items)
If you want a list to share the same items for all the meetings in a series, change the items into series items. If you don't change to series items, each meeting displays the list with just the items added for that date.
Meeting foras are a weird beast. To make a long story short: You can set a property on all lists and libraries that allow items in a list/doclib to be shared across meetings or to belong to a single meeting. SharePoint solves this by creating folders with meeting ID's (1, 2, 3 etc). and store items in those folders if they should only be shown for a specific meeting (for example Meeting Agenda).
If you disable this setting again, you will suddenly see the folders as you describe.
To solve this, either set the doclib back to be used for specific meetings, or manually move items from folders to root.
If you are provisioning lists into the meeting sites, let me know. I have a workaround for creating the lists programmatically using Remote Procedure Calls that allows for creating lists that share items across meetings.