Another potential issue is horizontal gene transfer, that is the ability for genes to be transfered to other species.
Which has absolutely nothing to do with genetic engineering. HGT happens, indeed it does, it's how we get things like pea aphids with fungus genes and sea slugs with algae genes, but it happens at an extremely small rate, and there is nothing particularly exceptional about a transgene that makes is any more or less to be transferred in such manner. That is a completely nonsensical line of thought that somehow HGT implies we should not use genetically engineered crops.
In practice, that means that some of those pesticide resistant genes may eventually end up in plants that are supposed to be killed by pesticides.
In theory, yes, it is possible that an herbicide resistance gene could jump to a weed species. In practice, that's not really a concern. The selection of herbicide resistant weed mutants is a very real and very serious problem, but that is a problem older than genetic engineering, does not occur via horizontal gene transfer, is not a problem intrinstic to GE crops but rather is due to poor resistance management strategies and over reliance (which is not the same as over use) on one mode of action of herbicide, and let me remind you, it is a problem because it threatens the benefits that those herbicide resistant crops already provide. Anti-GMO groups would have you believe that herbicide resistant crops are without benefit while simultaneously saying that herbicide resistant weeds which lessen the benefits of herbicide tolerant GMOs are these world ending 'superweeds'. In other words, they're bad because they have no benefits at all and they're bad because their benefits are diminishing. Talk about having your cake and eating it too.