I'm trying to automate snapshot checking DS free space. Its getting tricky for VMs with multiple DS attached. Script takes multiple snapshots for such VMs if condition satisfies. Please help me to understand where its going wrong.

Consolidating free space:

$free = (Get-Datastore -VM $vm | Select @{N="FreeSpace";E={[math]::Round(($_.FreeSpaceMB)*100/($_.CapacityMB),0)}})
Now checking if free space is available in each DS where VM connected:
foreach ($ds in $free.FreeSpace)
    if (($ds -gt 25)
get-vm $vm | new-snapshot -name "$cmr.$date" -Description $description
        
If I understand the question properly, regarding dealing with multiple datastores... I would take a look at introducing a Sort-Object after the initial Get-Datastore which is based on the FreeSpaceMB property, then only selecting the first datastore (which should have the least amount of free space available) and performing your calculation based on that. 
Untested example: 
$free = (Get-Datastore -VM $vm | Sort-Object -Property FreeSpaceMB | Select-Object -Property @{N="FreeSpace";E={[math]::Round(($_.FreeSpaceMB)*100/($_.CapacityMB),0)}} -First 1)
        
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