I'm going to take everything you wrote at face value.
Vanguard is an investment company. They do not and should not give tax advice. You should rely on a local, qualified tax preparer and not on Vanguard or me for tax advice.
Assuming that you're talking about a $6K contribution to a traditional IRA (very likely), and that you had enough earned income to support the contribution (very likely), and that you mean that you were in the MAGI phase out range for deductibility and were only able to deduct $1500 of that contribution, then:
You do not owe the 6% excise tax because you did not contribute more than the allowable contribution amount into your traditional IRA. Assuming you're too young for catchup contributions (very likely), your allowable contribution amount is the lesser of $6K or your earned income, so very likely $6K.
You are very likely eligible to deduct whatever fraction of your IRA contribution the tax software or you calculated. Let's assume it was $1500.
The remaining $4500 (or whatever the actual remainder amount is) of your contribution may stay in your IRA as a nondeductible contribution. You should have filed a Form 8606 with your 2019 tax return to reflect this nondeductible contribution.
If you have already filed your 2019 tax return (likely), you may file a 2019 Form 8606 by itself. You may owe a $50 penalty for not filing the form on a timely basis, although the penalty can be waived if you show reasonable cause for failure to file.
Going forward, that $4500 is a bit of a pain in the rear, because it affects the tax impacts of everything going forward that you do with all of your traditional IRAs. Your future withdrawals and Roth conversions are impacted on a pro-rata basis, and any heirs who inherit any of your IRAs will have their withdrawals impacted. I'm not sure how to get out of this "milk in the coffee" situation you are now in; perhaps others will chime in with suggestions.