in Sharepoint site collection is security boundary. Which means that each site collection has own collection of users (SPUser collection) and groups (SPGroup collection). I.e. if you remove specific user (SPUser) or group (SPGroup) from siteColA - it will be removed only in this siteColA site collection. If another site collection siteColB has SPUser which corresponds to the same user (or SPGroup which has the same name) - they will be kept untouched in siteColB.
For your specific problem - try to check target site's groups via PowerShell:
$site = Get-SPSite http://example.com
$site.RootWeb.SiteGroups
will these "broken" groups be shown in the output? If yes - try to remove it using PowerShell:
$groupName = ...
$site.RootWeb.SiteGroups.Remove($groupName)