When a phone number field has data put into it, it is up to the User to format it the way they deem appropriate. That is not the most user-friendly or data-centric approach. This is a good way to allow users to enter incorrect or sloppy data and cause possibly difficulty with search results while also affecting adoption. There are many other CRM platforms out there (At least 12 I could find) which will automatically format a telephone number. Hubspot does not currently have this basic feature.
Suggested solution: When a telephone number is typed into a phone field, the number should automatically format to the Contact's standardized country format with a country code in front of it. So, for US, +1 (555) 555-5555, for UK, +44 5555 555555, etc. Some countries do not have standardized formats, but widely accepted formats, or multiple formats depending on when the phone number was assigned. I do not know of an easy solution for that, but choosing one format or at the minimum, placing the correct country code in front of the numbers according to the selected country on the Contact or Company would be helpful. Possibly a non-editable drop-down with country abbreviation and code which auto-fills but is still selectable in case of error. This could also help with the calling feature if calling out of the country.
An admin User should be able to toggle in settings whether or not the field will auto format with country code. At the bare minimum, as a US based company, it should at least format any 10 digit numbers into standard US format (555) 555-5555.