For example, RSA is based on the integer factoring problem, but they are not equivalent. Vanilla RSA does not offer what they call "chosen-ciphertext security"; in fact, a careful plaintext padding scheme† is needed to approximate this property.
PKCS#1v1.5 padding is not that scheme††: it formats the plaintext with a fixed leading byte (or two). This puts implementers in a tricky spot - what do you do if you decrypt a message and the prefix is wrong? If your answer was "throw an error", then congratulations! You've completely compromised the security of RSA.
They reference this attack briefly on page two of the linked article; grep for "Bleichenbacher". For more information, you can find Bleichenbacher's description of his padding oracle attack on PKCS#1 here: http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.19..... I'll go further and say that implementing this attack is fun and enlightening - it's well worth your time.
† The scheme I'm alluding to is OAEP, but even it has implementation pitfalls that can sometimes be exploited.
†† But it is (bafflingly) the default padding scheme in every RSA library I can think of.