My name has "Mr" appended on airline ticket reservation. Would that cause problems at the airport?

Appending MR etc seems to be a trend (ie becoming more commonplace) for air tickets/boarding passes and, particularly when names are relatively long, this might be without a space. Examples:

Since very likely Aegean's custom, their staff should cope with interpreting this. The key point may be that the website you refer to does indeed recognise you correctly. Without a space it seems understandable that your forename is being interpreted as everything before the virgula suspensiva.

Attribution for the images above (in order):
http://www.a2zlifestyle.com/travel/the-best-day-to-book-airline-tickets/
http://www.india-forums.com/forum_posts.asp?TID=1204921&TPN=50
http://www.flickriver.com/photos/retokurmann/4124561291/

and for the one below that shows the use of MR long before 2001:
http://hostagencyreviews.com/airline-fare-types/

KLM mentions:

"No need to correct your name: ... If your ticket shows your names in a different order, without spaces and/or with ‘MR’, ‘MRS’ or ‘MS’ between your names – this is how names are shown in our systems...."

Don't worry, it's a common way of writing it and all personnel at the airport knows how this works.

I've worked in travel for over 10 years, so the rest of this post is based on that experience. In the "old times" airline reservation systems used to be white-on-blue screens full of cryptic codes and conventions. (And in fact, even though in many travel agencies better graphical interfaces are common, you can still see the "old-fashioned" displays even now - at the check-in desk of your airport they often still use these systems).

Some of these conventions, established many years ago to - presumably - reduce the amount of network traffic and the amount of text that operators have to key in, carry over in today's travel. The obvious ones are the use of flight numbers (almost all flights are codeshares which have about 4 different flight numbers for the same physical aircraft - if I had to redesign the system I would change that) and the use of three-letter codes to denote airports (e.g. AMS, LON, CDG, LAX). The naming convention is also one of these conventions. In these text-based systems, names are still entered in the form SURNAME/ABCMR or SURNAME/FIRSTNAMEMR (Nowadays, for "security reasons", airlines usually require the full first name). One advantage is that the surname of passengers in the same booking only needs to be entered once, e.g. SURNAME/ALBERTMR/JENNAMRS/JOHNCHD (Again, security is now quoted as the reason that women need to provide their maiden name - one of the major causes of people being denied check-in is that they automatically provide their married name which is not necessarily the one in their passport).

I know that some systems (like Amadeus) also support an optional space: SURNAME/FIRSTNAME MR. Often in passenger-facing documents, such as travel schedules and boarding passes, this is automatically converted to Mr. Firstname Surname, just as the cryptic CDGLAX is also printed as "Paris Charles-de-Gaulle - Los Angeles Intl.". However, as I explained above, the space is optional (GEORGIOSMR or GEORGIOS MR are both allowed). Apparently the website that they gave you, which (in simple terms) is just a front-end that reads the information from the same text-based system, is not smart enough to recognize the title without the space. Had your reservation agent added the space, it would probably have converted it correctly. However, and to answer your question:

Is it likely that they'll think "mr" is part of the name of the ticket's owner?

-- no, to an agent or customs officer at the airport who are used to reading the "cryptic" form, it will not be a problem.

It is standard policy by Aegean (and other companies) to append Mr or Mrs on the first name of each passenger, depending of the gender of the passenger. For example, all my tickets write CHARALAMPOSMR FANOULIS

I would make sure you have supporting evidence of making the booking, eg have your credit / debit card that you made the booking with.

When you Check-In, ask the Check-In staff to make sure that your name is printed correctly on the Boarding Pass. If you have problems with Security onto the plane they will usually just ask you to return to the Check-In desk and have your Boarding Pass name altered.