The gemara says that when the sharecropper deviates and plants barley when he was supposed to plant wheat, it is considered to be the loss of the sharecropper, because the owner can claim (as rashi explains) that he was davening for success for wheat, not for barley. Rashi is very meduyak - ואני לא בקשתי מן השמים בתחילת השנה שיצליחני בשעורים אלא בחטין
The focus on the "beginning of the year" is that even though the land owner realizes that the sharecropper planted barley rather than wheat and from the time of planting he was davening for barley, he can still claim before the planting season he has already been davening to Hashem for success in wheat, not barley and perhaps that is the tefillah that would have been listened to.
This idea that the tefillah will only work for what you are davening for explicitly and not merely what you are intending for is found in rashi in chumach (parshas chukas 21:1) - וישמע הכנעני מלך ערד, where rashi explains that they were amaleikim dressed as Cananim so that the Jews should daven that they should defeat Canan when in fact they were fighting with amaleik so their tefillah would be useless. The Mesech Chochma makes the connection to our gemara. He explains that even though they would have surely davened against amaleik had they known that it was amaleik, tefillah doesn't work when you are davening for the wrong thing. If not for our gemara it could be that the cheshbon of the amaleikim was wrong and the tefillah does in fact work, but from our gemara we see that their cheshbon was actually correct.
We learn from here that when we daven, although it is important to make the tefillah specific (as we see from chazal in the way the instituted the shemoneh esrei asking for specific requests, not just "all good things" - this is also clear from tosafo d.h. l'nisah, that if one davens very generally for success, it is not a strong tefillah so Hashem is less likely to listen and he therefore has no claim, but when he davens for something specific Hashem is more likely to listen and therefore he has a claim), we should leave our tefillos open enough so that if we are mistaken about certain facts, the tefillah will still be applicable, rather than limiting the tefillah based on facts that will be realized to be wrong rendering the entire tefillah futile.