The score is calculated from the particular formula which is based on the number of errors and tags as well as the type of tags. It is a point-deduction system. Each error has a different severity and the more critical the error is, the more points will be deducted. Some errors do not deduct any point. When there are many errors in less tags, the more points will be deducted.

If you get extremely low score even with enough efforts, your DOCTYPE declaration may not be appropriate. You always need to be aware that which HTML you are writing. Also, please note that it could stop validation when too many errors are detected. You may want to uncheck certain items to exclude them from validation.

You do not have to get disappointed or upset about low score. There is no scholarly evidence with the formula and it is just a grammatical(and a little religious) checking.
Even a nice-looking website often has messy grammar and such a website only looks good in certain environments. Your website will never look worse by correcting grammar.

It is easy to get a perfect score if you exclude many items to be checked, but that makes no sense. You should not exclude any items except religious ones.
Getting a perfect score does not mean it is great HTML. It does not guarantee your website will look perfect in every www browser either. Please do not find the score reassuring. Good contents are always required besides good HTML to be a better website.
FYI: please do not consider this Another HTML-lint 5's HTML as a good example.

Although it depends on the person, using authoring tools such as HTML editors is obviously efficient than writing codes from scratch. Unfortunately, however, such HTML editors often generate grammatically wrong HTML . (Style Guide for online hypertext is just being cynical).

There is a possiblity that ridiculous scores could be displayed due to a trouble in programming. Please contact to support@xyxon.co.jp in case of getting the same errors repeatedly.