It never hurts to some data validation before using what comes from a file. Try this:
Get-content user.txt |
Foreach-Object {
If ($_.Trim().Length -gt 3){
$user = $_.Trim()
Get-aduser -filter {mail -like $user} -server My-GC-fqdn:3268 -properties * |
Select-Object name, co
}
} | Export-csv country.csv -NoTypeInfo
Using the pipeline eliminates the need for the "-append" on the Export-CSV, too.