Since you are on this website I assume you own a computer, unless you have to go to a library to use one. If you do have a computer then spent the money, about $30-$40 dollars and get the software. It is more simple to use than programming by hand. You can then see what you have programmed into one list. As someone else mentioned, you can then import, from the Radio Reference database, radio systems that can be a bit complex and confusing at times. The result is far fewer problems with how things work and the time saved is enormous. I like the Starrsoft software for the GRE, Radio Shack scanners. I don't use any of the free software as the Starrsoft is more intuitive and organized better. As well, I like how it looks.
Being able to see how all the channels are entered into the radio makes finding mistakes far easier than using the radio manually. Can you proof read an entire page of writing word by word or sentence by sentence? No, because you can't see the big picture. Why then try to program a scanner channel by channel. If I want to make sure my PSR-500 will turn on the display light on every channel, I hit select all and hit one button and know that every channel will light up on each reception. If I know every frequency needs to be set to Narrow FM I do the same. If I have an agency that uses all CTCSS or is a conventional digital with NAC's I just highlight the channels of that system and enter hit one button thus saving a lot of time entering NAC channel by channel and will probably make a mistake if I program channel by channel.
I'm not entirely sure how one object duplicated on other scan lists as I rarely program my scanners manually, but if you figured out how to stop it, then great. The advantage of being able to include one object in several lists is to use the memory more efficiently. For example, in California there are two universal frequencies in every law enforcement VHF High radio, CLEMARS (California Law Enforcement Mutual Aid Radio System) and CALCORD (California Coordination). They need to be in every public state/local list I have in my radios, which is usually 14-16 lists per file I'm able to include these in multiple lists without reprogramming them in each list.
The small amount of money spent on software would have prevented the problem you related here and will prevent many other problems. I have 18 files of more than 1000-1600 objects and more. I have one for each area in California, Arizona and Nevada. The other two files are chosen from New Mexico, Colorado and Oregon and I put those into the two files I keep open on the radio for the places I visit infrequently. I have enough trouble keeping these up to date and could not possibly accomplish without computer software.