Unfortunately, this doesn’t compare the columns included in the index, just the indexes by name. I’ll bang one together that does that latter. You’ll need sqlpsx in order to run this.
cls
$srcTables = Get-SqlTable $(Get-SqlDatabase -sqlserver "SourceServer" -dbname "SrcDB")
$targetTables = Get-SqlTable $(Get-SqlDatabase -sqlserver "TargetServer" -dbname "TargetDB")
foreach($table in $srcTables)
{
$targetTable = $targetTables | where{$_.Name -eq $table.Name}
$targetIDX = $targetTable.Indexes;
$srcIDX = $table.Indexes;
$diff = Compare-Object -ReferenceObject $srcIDX -DifferenceObject $targetIDX -Property Name
if($diff -ne $null)
{
Write-Host $diff
}
}
This script does compare the index columns, but I haven’t put the two together yet. I need to clean up my scripts. 
function CheckIndexColumns($table, $index)
{
$columns = $index.IndexedColumns# | Sort-Object -Property Name
foreach($idx in $table.Indexes | where{$_.Name -ne $index.Name})
{
#if($idx.IndexedColumns.Count -ne $index.IndexedColumns.Count){continue;}
#$sourceCols = $index.IndexedColumns | Sort-Object -Property Name
$targetCols = $idx.IndexedColumns #| Sort-Object -Property Name
$diff = Compare-Object -ReferenceObject $columns -DifferenceObject $targetCols -SyncWindow 1000
if($diff -eq $null)
{
Write-Host "Possible duplicate index found on table Table: $($table.Name)" -ForegroundColor Red
write-Host "Index [$($index.Name)] and index [$($idx.Name)] have the same columns: $($idx.IndexedColumns)" -ForegroundColor DarkCyan
}
}
}
cls
$db = Get-SqlDatabase -sqlserver ServerName -dbname DatabaseName
foreach($table in $db.Tables)
{
Write-Host "Checking table $($table.Name)..." -ForegroundColor Gray
foreach($idx in $table.Indexes)
{
CheckIndexColumns $table $idx
}
}
Sql Server Powershell 