Unfortunately, this does happen in very juiced maps, with a ton of items on the ground, especially if you're doing a strat where you run a lot of quant, or have a magic find character, but there are some things you can do to improve it. It's not intentional, it's just the plugin 'lagging', either because your performance settings are too low, or because you have very high cpu usage from POE.
Under Core>Performance change 'threads count' and 'target parallel coroutine fps'. The plugin uses these settings to scan for 'entities' to click. I'd recommend having at least 2 threads, and 180 parallel coroutine, but i'm still testing around with it to get the best values for me. It may just be best to set the 'parallel' to your monitor refresh rate * threads count, but again i'm not entirely sure. Here are the settings I have and they work fine for me, but you'll likely want to change them to suit your pc:
Loader_y5uBQCcp0w.jpg. The higher the 'parallel' value, the more often the plugin will try to update the location of entities, causing higher cpu usage, and more lag, because your cpu usage. However, the lower the value, the less frequently it will update the location, causing what you're describing, where the plugin is trying to click on items that have already been picked up. It's a balancing act between finding the point that your cpu usage is good, while not missclicking much. The last version also fixed an issue that caused delays with clicking, so make sure you're using the latest one.
Edit: With 'Added entities multi-threading' on, you'll get some harmless debug text occasionally in the corner saying that threads are being stopped, it's fine, I just ignore them. If you want to get rid of them, disable that, but you might get worse performance.
Edit2: If nothing helps, and pickit is working better for you, you could just disable click items in ClickIt, then use PickIt to pick up items. Those settings should help though.