How should I interpret "English is poor" review when I used a language check service before submission?

There are several possibilities here, although generally they all have the same solution.

The English is poor or incorrect and the company did not check it well

It is possible that the company that checked your article did a bad job. This happens. Maybe the service did not have a native English speaker check your article. Maybe they had a bad day. Maybe they don't provide good service, and you just got lucky on previous times. It's hard to say.

The English is grammatical, but not idiomatic

It is possible that the company that checked your article fixed all the grammatical mistakes, but that there are still some phrasings which are not idiomatic or particularly natural. This is essentially a function of how detailed the corrections were. For example, here is the first paragraph of your post:

Recently I had submitted a Manuscript to an International Journal. Though it is accepted as a Minor revision, but I am worried about the reviewer's comment. First reviewer has commented that the Paper is well written, still needs some English improvements. Second reviewer has also commented that English improvements is required.

There are some small grammatical errors, and I can correct them as follows (in bold):

Recently I had submitted a manuscript to an international journal. Though it is was accepted as a minor revision, but I am worried about the reviewer's comment. The first reviewer has commented that the paper is well written, but still needs some English improvements. The second reviewer has also commented that English improvements is are required.

While this paragraph is now grammatically correct, it still does not feel like it was written by a native speaker, and the way some words are used is a little odd. (E.g. using though and but in the second sentence; you really only need one of them.) So, a more thorough checking would suggest edits like the following:

Recently I had submitted a manuscript to an international journal. Though it is was accepted as a Minor revision pending minor revisions, but I am worried about the reviewers's comments. The first reviewer has commented that the paper is well written, but still needs some English improvements. The second reviewer has also commented that English improvements is are required.

The checking service could have done the first step (making it grammatically correct) without following through on the second step (making it idiomatic). The second step is much harder, of course, as it requires knowledge of what style is appropriate for your field (and for the journal you are writing for), and, to some extent, it requires technical knowledge of whatever you're writing about.

The English is fine, the reviewer is just being picky

Academic articles are complex and often involve detailed theoretical or technical discussion. At times, they can be hard to follow. Sometimes this complexity is interpreted as poor language skills, and reviewers complain. I know more than one native English speaker who has received reviews asking them to check their article with a native speaker. In essence, this criticism relates to how the content is presented rather than linguistic concerns like grammaticality or phrasing.

The solution

It is not easily possible for you to determine right now which of the above scenarios has happened. However, a big help would be for you to show the manuscript to a trusted colleague who is a native speaker of English, and ask them how it reads. If the English is really atrocious, then you know you have a problem with the checking service; if there are some unusual phrases but it's otherwise fine, then you know the problem is that it's occasionally un-idiomatic; and if there are no obvious problems, then it's probably just an issue of reviewer interpretation.

The other step you should take is to re-read your manuscript and attempt to make complex exposition more clear. (This is a step I advise everyone to do at basically every stage of the writing process...) This will help your article in the case that the English was fine but the reviewer was just confused.

Finally, breathe and relax. Your article was accepted, congratulations! Clearly the reviewers and the editor thought that the scientific content was sufficient to merit publication.

Is it a common comment that all reviewers do?

It's a comment I saw several times at the beginning of my career, but with a little attention it became rarer and rarer.

I think that there can be two issues.

First, as remarked by ff524, if you modify the text after the language check, you can introduce errors that go undetected. I'm a non-native English speaker too, but I can recognize many grammar errors in your question: don't take it as a judgement, but you really ought to consider that you might have introduced new errors.

Second, the English proofreader likely lacks the technical knowledge to understand the details of your manuscript, and they might involuntarily introduce other errors.

As a non-native speaker, I frequently use the correction service freely offered by my university; however, I work side by side with the proofreader to explain the technical usage of certain words. For instance, in my field, we use the word realization with an uncommon acceptation (you can find an explanation in this answer on Physics.SE) which typically makes the proofreader comment: "Are you sure that you want to use realization here?". A proofreader left alone would probably modify realization with a technically incorrect word.

Here are my 2 cents:

1. Work together with the proofreader.
2. Avoid modifying the text after the last check, until you have improved your mastery of English.

Unfortunately, there is not much to interpret. If the reviewers found your English to be below the journal's standard, you really have no other choice than to accept this. Language standards seem to differ somewhat between different journals, with some being stricter than others, and in general the comment that you received is not simply a default (see this answer for details).

Since you were asked to make "minor revisions", there won't be another round of reviewing. You will most likely have to briefly explain those revisions in your cover letter, but ultimately it is up to you how much work you put into them.

Another question altogether is how to improve the language of the manuscript or whether you could get a refund from the editing service. There are various answer to questions like these on this site (1, 2, 3, 4).