Is there a contradiction between the verse: "Invite to the way of your Lord with wisdom and good instruction" and the verse: "Fight those who do not believe in Allah or in the Last Day from among those who were given the Scripture"?

There is no contradiction between the two verses. The first verse was revealed in Mecca, commanding the appeasement of the Quraysh and inviting them gently. It is an abrogating verse concerning disobedient monotheists, and it is abrogated by the verse of fighting regarding disbelievers. It is also said that it is an abrogating verse concerning disbelievers whose guidance is hoped for. Wisdom is interpreted as the Qur’an, and good admonition as encouraging and deterring or gentle speech. Arguing in the best manner means refraining from harm and not falling short in conveying the message, and this has been abrogated by the verse of fighting.