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I'm experiencing a strange issue here where the price navigation filter (layered navigation) somehow came up with negative price ranges.

If I flush the price tables it seems to solve the problem, until next time prices get re-indexed. Then the negative price ranges re-appear.

Another issue is that the price ranges are not even accurate. It would show the following: CA$0.00 - CA$9.99 (2) - as if there are 2 items within this price range. But we do not have any items priced within this price range...

Help please!!

The solution documented here works for me, although I didn't test it thoroughly:

Rewrite the following file using the correct class rewrite procedure, and perform an price reindex subsequently.

File:
vendor/magento/module-configurable-product/Model/ResourceModel/Product/Indexer/Price/Configurable.php

Method:
_applyConfigurableOption()

Replace:

$select->columns(
 [
 'min_price' => new Zend_Db_Expr('i.min_price - i.orig_price + io.min_price'),
 'max_price' => new Zend_Db_Expr('i.max_price - i.orig_price + io.max_price'),
 'tier_price' => 'io.tier_price',
 ]
);

With:

$select->columns(
 [
 'min_price' => new Zend_Db_Expr('io.min_price'),
 'max_price' => new Zend_Db_Expr('io.max_price'),
 'tier_price' => 'io.tier_price'
 ]
);

For Magento 2.2.x

This is not a code but a data issue. In most cases it can appears when you use direct (used SQL queries) product import tools.
I've taken one configurable product with negative min_price and max_price, imported with special prices and dropped special price for it and it's child products. After re-index I haven't seen any results, and only after saving this configurable product from admin, I saw the changes. It shows, that direct special prices import doesn't trig some important index processes. It still incorrect:

but it shows a bug.
E.g. I took another product without any special prices for itself and its' child products, and set it special price for some option. After re-index everything looked fine:

So, check that products that you import don't have special price (at least configurable products), or change your import tool.